Agricultural and Biological Sciences › Plant Science

Chromosomal and Genetic Variations

Works Count: 60457

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Description

This cluster of papers explores the evolution of plant genomes, with a focus on polyploidy, transposable elements, small RNAs, and the role of repetitive elements. It investigates the impact of genome duplication on genetic diversity, speciation, and epigenetic regulation, shedding light on the evolutionary significance of these processes in plants.

Keywords

Genome Evolution; Polyploidy; Transposable Elements; Plant Speciation; Small RNAs; Centromeres; Genetic Diversity; Chromosome Duplication; Epigenetic Regulation; Repetitive Elements

Origin and evolution of retroelements based upon their reverse transcriptase sequences.

1990-10-01

Yue Xiong , Thomas H. Eickbush

A stable genomic source of P element transposase in Drosophila melanogaster.

1988-03-01

Hugh M. Robertson , Christine R Preston , R W Phillis +3 more

Abstract A single P element insert in Drosophila melanogaster, called P[ry+ delta 2-3](99B), is described that caused mobilization of other elements at unusually high frequencies, yet is itself remarkably stable. … Abstract A single P element insert in Drosophila melanogaster, called P[ry+ delta 2-3](99B), is described that caused mobilization of other elements at unusually high frequencies, yet is itself remarkably stable. Its transposase activity is higher than that of an entire P strain, but it rarely undergoes internal deletion, excision or transposition. This element was constructed by F. Laski, D. Rio and G. Rubin for other purposes, but we have found it to be useful for experiments involving P elements. We demonstrate that together with a chromosome bearing numerous nonautonomous elements it can be used for P element mutagenesis. It can also substitute efficiently for "helper" plasmids in P element mediated transformation, and can be used to move transformed elements around the genome.

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The Probability of Duplicate Gene Preservation by Subfunctionalization

2000-01-01

Michael Lynch , Allan Force

Abstract It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members … Abstract It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 105 or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.

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The Significance of Responses of the Genome to Challenge

1984-11-16

Barbara McClintock

From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish, From asymmetrical to balanced genomic diversification during rediploidization: Subgenomic evolution in allotetraploid fish,

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

2014-08-21

Boulos Chalhoub , France Denœud , Shengyi Liu +7 more

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more … Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

2007-03-01

Julius Brennecke , Alexei A. Aravin , Alexander Stark +4 more

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A germline-specific class of small RNAs binds mammalian Piwi proteins

2006-06-04

Angélique Girard , Ravi Sachidanandam , Gregory J. Hannon +1 more

Degenerate oligonucleotide-primed PCR: General amplification of target DNA by a single degenerate primer

1992-07-01

H. Telenius , Nigel P. Carter , Charlotte E. Bebb +3 more

Transposable elements and the epigenetic regulation of the genome

2007-03-16

R. Keith Slotkin , Robert A. Martienssen

Ancestral polyploidy in seed plants and angiosperms

2011-04-08

Yuannian Jiao , Norman J. Wickett , Saravanaraj Ayyampalayam +7 more

The B73 Maize Genome: Complexity, Diversity, and Dynamics

2009-11-20

Patrick S. Schnable , Doreen Ware , Robert S. Fulton +7 more

A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) … A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078 ) have sequenced the Palomero Toluqueño ( Palomero ) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118 ) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115 ) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole ).

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A simple and rapid method for the preparation of plant genomic DNA for PCR analysis

1991-01-01

Keith J. Edwards , CN Johnstone , C. Thompson

Journal Article A simple and rapid method for the preparation of plant genomic DNA for PCR analysis Get access K. Edwards, K. Edwards Plant Biotechnology Section, ICI Seeds, Jealott's Hill … Journal Article A simple and rapid method for the preparation of plant genomic DNA for PCR analysis Get access K. Edwards, K. Edwards Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Johnstone, C. Johnstone Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Thompson C. Thompson Plant Biotechnology Section, ICI Seeds, Jealott's Hill Research StationBracknell, Berks, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 6, 25 March 1991, Page 1349, https://doi.org/10.1093/nar/19.6.1349 Published: 25 March 1991 Article history Accepted: 02 January 1991 Published: 25 March 1991

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Estimation of nuclear DNA content in plants using flow cytometry

2007-09-01

Jaroslav Doležel , Johann Greilhuber , Jan Suda

Rfam: annotating non-coding RNAs in complete genomes

2004-12-17

Sam Griffiths‐Jones

Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new … Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/ .

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Selfish genes, the phenotype paradigm and genome evolution

1980-04-01

W. Ford Doolittle , Carmen Sapienza

Mobile Elements: Drivers of Genome Evolution

2004-03-11

Haig H. Kazazian

Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped … Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.

The impact of retrotransposons on human genome evolution

2009-09-18

Richard Cordaux , Mark A. Batzer

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LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

2008-01-14

David Ellinghaus , Stefan Kurtz , Ute Willhoeft

Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed … Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. Therefore, there is a considerable demand for computational identification of transposable elements. LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs).We have developed a software tool LTRharvest for the de novo detection of full length LTR retrotransposons in large sequence sets. LTRharvest efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of LTRharvest against a gold standard annotation for Saccharomyces cerevisae and Drosophila melanogaster shows a sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. This is comparable or slightly better than annotations for previous software tools. The main advantage of LTRharvest over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software.LTRharvest is an efficient software tool delivering high quality annotation of LTR retrotransposons. It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes LTRharvest a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.

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A unified classification system for eukaryotic transposable elements

2007-11-06

Thomas Wicker , François Sabot , Aurélie Hua‐Van +7 more

A second-generation linkage map of the human genome

1992-10-01

Jean Weissenbach , Gàbor Gyapay , Colette Dib +5 more

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

2004-10-01

Olivier Jaillon , Jean‐Marc Aury , Frédéric Brunet +7 more

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Repbase Update, a database of eukaryotic repetitive elements

2005-01-01

Jerzy Jurka , Vladimir V. Kapitonov , Adam Pavlı́ček +3 more

Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which … Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html.

Alu repeats and human genomic diversity

2002-05-01

Mark A. Batzer , Prescott L. Deininger

Nested Retrotransposons in the Intergenic Regions of the Maize Genome

1996-11-01

Phillip SanMiguel , Alexander P. Tikhonov , Young-Kwan Jin +7 more

The relative organization of genes and repetitive DNAs in complex eukaryotic genomes is not well understood. Diagnostic sequencing indicated that a 280-kilobase region containing the maize Adh1 -F and u22 … The relative organization of genes and repetitive DNAs in complex eukaryotic genomes is not well understood. Diagnostic sequencing indicated that a 280-kilobase region containing the maize Adh1 -F and u22 genes is composed primarily of retrotransposons inserted within each other. Ten retroelement families were discovered, with reiteration frequencies ranging from 10 to 30,000 copies per haploid genome. These retrotransposons accounted for more than 60 percent of the Adh1 -F region and at least 50 percent of the nuclear DNA of maize. These elements were largely intact and are dispersed throughout the gene-containing regions of the maize genome.

Rapid isolation of high molecular weight plant DNA

1980-01-01

Michael G. Murray , William F. Thompson

A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete … A method is presented for the rapid isolation of high molecular weight plant DNA (50,000 base pairs or more in length) which is free of contaminants which interfere with complete digestion by restriction endonucleases. The procedure yields total cellular DNA (i.e. nuclear, chloroplast, and mitochondrial DNA). The technique is ideal for the rapid isolation of small amounts of DNA from many different species and is also useful for large scale isolations.

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LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

2007-05-08

Zhigang Xu , Hao Wang

Long terminal repeat retrotransposons (LTR elements) are ubiquitous eukaryotic transposable elements. They play important roles in the evolution of genes and genomes. Ever-growing amount of genomic sequences of many organisms … Long terminal repeat retrotransposons (LTR elements) are ubiquitous eukaryotic transposable elements. They play important roles in the evolution of genes and genomes. Ever-growing amount of genomic sequences of many organisms present a great challenge to fast identifying them. That is the first and indispensable step to study their structure, distribution, functions and other biological impacts. However, until today, tools for efficient LTR retrotransposon discovery are very limited. Thus, we developed LTR_FINDER web server. Given DNA sequences, it predicts locations and structure of full-length LTR retrotransposons accurately by considering common structural features. LTR_FINDER is a system capable of scanning large-scale sequences rapidly and the first web server for ab initio LTR retrotransposon finding. We illustrate its usage and performance on the genome of Saccharomyces cerevisiae. The web server is freely accessible at http://tlife.fudan.edu.cn/ltr_finder/.

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The advantages and disadvantages of being polyploid

2005-10-11

Luca Comai

Hypervariable ‘minisatellite’ regions in human DNA

1985-03-01

Alec J. Jeffreys , Victoria Wilson , Swee Lay Thein

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

2003-03-01

John Bowers , Brad Chapman , Junkang Rong +1 more

Transposition of Cloned P Elements into Drosophila Germ Line Chromosomes

1982-10-22

Allan C. Spradling , Gerald M. Rubin

Recombinant DNA carrying the 3-kilobase transposable element was injected into Drosophila embryos of a strain that lacked such elements. Under optimum conditions, half of the surviving embryos showed evidence of … Recombinant DNA carrying the 3-kilobase transposable element was injected into Drosophila embryos of a strain that lacked such elements. Under optimum conditions, half of the surviving embryos showed evidence of P element-induced mutations in a fraction of their progeny. Direct analysis of the DNA of strains derived from such flies showed them to contain from one to five intact 3-kilobase P elements located at a wide variety of chromosomal sites. DNA sequences located outside the P element on the injected DNA were not transferred. Thus P elements can efficiently and selectively transpose from extrachromosomal DNA to the DNA of germ line chromosomes in Drosophila embryos. These observations provide the basis for efficient DNA-mediated gene transfer in Drosophila.

A high-resolution recombination map of the human genome

2002-06-10

Augustine Kong , Daníel F. Guðbjartsson , Jesús Sainz +7 more

High density molecular linkage maps of the tomato and potato genomes.

1992-12-01

Steven D. Tanksley , Martin W. Ganal , James P. Prince +7 more

Abstract High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the … Abstract High density molecular linkage maps, comprised of more than 1000 markers with an average spacing between markers of approximately 1.2 cM (ca. 900 kb), have been constructed for the tomato and potato genomes. As the two maps are based on a common set of probes, it was possible to determine, with a high degree of precision, the breakpoints corresponding to 5 chromosomal inversions that differentiate the tomato and potato genomes. All of the inversions appear to have resulted from single breakpoints at or near the centromeres of the affected chromosomes, the result being the inversion of entire chromosome arms. While the crossing over rate among chromosomes appears to be uniformly distributed with respect to chromosome size, there is tremendous heterogeneity of crossing over within chromosomes. Regions of the map corresponding to centromeres and centromeric heterochromatin, and in some instances telomeres, experience up to 10-fold less recombination than other areas of the genome. Overall, 28% of the mapped loci reside in areas of putatively suppressed recombination. This includes loci corresponding to both random, single copy genomic clones and transcribed genes (detected with cDNA probes). The extreme heterogeneity of crossing over within chromosomes has both practical and evolutionary implications. Currently tomato and potato are among the most thoroughly mapped eukaryotic species and the availability of high density molecular linkage maps should facilitate chromosome walking, quantitative trait mapping, marker-assisted breeding and evolutionary studies in these two important and well studied crop species.

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Genome evolution in polyploids.

2000-01-01

Jonathan F. Wendel

PATHWAYS, MECHANISMS, AND RATES OF POLYPLOID FORMATION IN FLOWERING PLANTS

1998-11-01

Justin Ramsey , Douglas W. Schemske

▪ Abstract Polyploidy is widely acknowledged as a major mechanism of adaptation and speciation in plants. The stages in polyploid evolution include frequent fertility bottlenecks and infrequent events such as … ▪ Abstract Polyploidy is widely acknowledged as a major mechanism of adaptation and speciation in plants. The stages in polyploid evolution include frequent fertility bottlenecks and infrequent events such as gametic nonreduction and interspecific hybridization, yet little is known about how these and other factors influence overall rates of polyploid formation. Here we review the literature regarding polyploid origins, and quantify parameter values for each of the steps involved in the principal pathways. In contrast to the common claim that triploids are sterile, our results indicate that the triploid bridge pathway can contribute significantly to autopolyploid formation regardless of the mating system, and to allopolyploid formation in outcrossing taxa. We estimate that the total rate of autotetraploid formation is of the same order as the genic mutation rate (10 −5 ), and that a high frequency of interspecific hybridization (0.2% for selfing taxa, 2.7% for outcrossing taxa) is required for the rate of tetraploid formation via allopolyploidy to equal that by autopolyploidy. We conclude that the rate of autopolyploid formation may often be higher than the rate of allopolyploid formation. Further progress toward understanding polyploid origins requires studies in natural populations that quantify: (a) the frequency of unreduced gametes, (b) the effectiveness of triploid bridge pathways, and (c) the rates of interspecific hybridization.

The genome of the mesopolyploid crop species Brassica rapa

2011-08-28

Xiaowu Wang , Hanzhong Wang , Jun Wang +7 more

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De novo identification of repeat families in large genomes

2005-06-01

Alkes L. Price , N C Jones , Pavel A. Pevzner

Every time we compare two species that are closer to each other than either is to humans, we get nearly killed by unmasked repeats. Every time we compare two species that are closer to each other than either is to humans, we get nearly killed by unmasked repeats.

Translocation of the c-myc gene into the immunoglobulin heavy chain locus in human Burkitt lymphoma and murine plasmacytoma cells.

1982-12-01

Rebecca Taub , Ilan R. Kirsch , Cynthia C. Morton +5 more

The consistent appearance of specific chromosomal translocations in human Burkitt lymphomas and murine plasmacytomas has suggested that these translocations might play a role in malignant transformation. Here we show that … The consistent appearance of specific chromosomal translocations in human Burkitt lymphomas and murine plasmacytomas has suggested that these translocations might play a role in malignant transformation. Here we show that transformation of these cells is frequently accompanied by the somatic rearrangement of a cellular analogue of an avian retrovirus transforming gene, c-myc. Moreover, we map c-myc to human chromosome 8 band q24, the chromosomal segment involved in the reciprocal Burkitt translocations [t(8;14), t(8;22) and t(2;8)]. In two t(8;14) human Burkitt cell lines, c-myc appears to have been translocated directly into a DNA restriction fragment that also encodes the immunoglobulin mu chain gene. In the case of a specific cloned fragment of DNA derived from a mouse plasmacytoma, we demonstrate directly that c-myc has been translocated into the immunoglobulin alpha switch region. Our data provide a molecular basis for considering the role that specific translocations might play in malignant transformation.

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Molecular Reconstruction of Sleeping Beauty, a Tc1-like Transposon from Fish, and Its Transposition in Human Cells

1997-11-01

Zoltán Ivics , Perry B. Hackett , Ronald H.A. Plasterk +1 more

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

2004-01-01

LaDeana W. Hillier , Webb Miller , Ewan Birney +7 more

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to … We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

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POLYPLOID INCIDENCE AND EVOLUTION

2000-12-01

Sarah P. Otto , Jeannette Whitton

▪ Abstract Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates … ▪ Abstract Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immediate shifts in morphology, breeding system, and ecological tolerances. Theoretical models support the potential for increased adaptability in polyploid lineages. The evidence suggests that polyploidization can produce shifts in genetic systems and phenotypes that have the potential to result in increased evolutionary diversification, yet conclusive evidence that polyploidy has changed rates and patterns of diversification remains elusive.

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The map-based sequence of the rice genome

2005-08-01

Takuji Sasaki

GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism

1995-05-01

Michel Raymond , François Rousset

Journal Article GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism Get access M. Raymond, M. Raymond Institut des Sciences de l'Evolution, URA CNRS 327, Laboratoire de Genetique … Journal Article GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism Get access M. Raymond, M. Raymond Institut des Sciences de l'Evolution, URA CNRS 327, Laboratoire de Genetique et Environnement, Universite de Montpellier II (CC 065)Place E. Bataillon, 34095 Montpellier cedex 05, France Search for other works by this author on: Oxford Academic PubMed Google Scholar F. Rousset F. Rousset Institut des Sciences de l'Evolution, URA CNRS 327, Laboratoire de Genetique et Environnement, Universite de Montpellier II (CC 065)Place E. Bataillon, 34095 Montpellier cedex 05, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 86, Issue 3, May 1995, Pages 248–249, https://doi.org/10.1093/oxfordjournals.jhered.a111573 Published: 01 May 1995 Article history Received: 28 March 1994 Accepted: 04 October 1994 Published: 01 May 1995

Phased diploid genome assembly with single-molecule real-time sequencing

2016-10-17

Chen-Shan Chin , Paul Peluso , Fritz J. Sedlazeck +7 more

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The evolutionary significance of polyploidy

2017-05-15

Yves Van de Peer , Eshchar Mizrachi , Kathleen Marchal

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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

2019-03-22

Parysatis Sachs , Dong Ding , Philipp Bergmaier +6 more

Abstract Endogenous retroviruses (ERVs) can confer benefits to their host but present a threat to genome integrity if not regulated correctly. Here we identify the SWI/SNF-like remodeler SMARCAD1 as a … Abstract Endogenous retroviruses (ERVs) can confer benefits to their host but present a threat to genome integrity if not regulated correctly. Here we identify the SWI/SNF-like remodeler SMARCAD1 as a key factor in the control of ERVs in embryonic stem cells. SMARCAD1 is enriched at ERV subfamilies class I and II, particularly at active intracisternal A-type particles (IAPs), where it preserves repressive histone methylation marks. Depletion of SMARCAD1 results in de-repression of IAPs and adjacent genes. Recruitment of SMARCAD1 to ERVs is dependent on KAP1, a central component of the silencing machinery. SMARCAD1 and KAP1 occupancy at ERVs is co-dependent and requires the ATPase function of SMARCAD1. Our findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence ERVs. This reveals ATP-dependent chromatin remodeling as an integral step in retrotransposon regulation in stem cells and advances our understanding of the mechanisms driving heterochromatin establishment.

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RepeatModeler2 for automated genomic discovery of transposable element families

2020-04-16

Jullien M. Flynn , Robert Hubley , Clément Goubert +4 more

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types … The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license ( https://github.com/Dfam-consortium/RepeatModeler , http://www.repeatmasker.org/RepeatModeler/ ).

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The complete sequence of a human genome

2022-03-31

Sergey Nurk , Sergey Koren , Arang Rhie +7 more

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the … Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

2004-12-09

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PEN1 catalyses RNA primer removal during plastid DNA replication in maize

2025-06-25

Xing Huang , Guolong Shi , Qiao Xiao +7 more | Nature Plants

Retrotransposon 3S18 forms self-protective aggregates and prolongs mid-oogenesis

2025-06-24

Dan Shen , Yaqian Xu , Qi Shi +5 more | Cell Reports

Nonapeptide molecular evolution during the adaptive radiation of Tanganyika cichlids

2025-06-24

Pol Sorigue , Walter Salzburger , Rui F. Oliveira | bioRxiv (Cold Spring Harbor Laboratory)

Abstract Oxytocin (OT) and vasotocin (VT) are evolutionarily conserved nonapeptides that regulate a wide range of physiological and behavioural processes in vertebrates. Their receptor families have undergone gene duplications that … Abstract Oxytocin (OT) and vasotocin (VT) are evolutionarily conserved nonapeptides that regulate a wide range of physiological and behavioural processes in vertebrates. Their receptor families have undergone gene duplications that facilitated functional diversification throughout vertebrate evolution. Using the diverse cichlid species in Lake Tanganyika, which have undergone repeated evolutionary transitions between social phenotypes, we investigated the molecular evolution of the nonapeptide system and its potential involvement in social behaviour. We performed a positive selection analysis based on the dN/dS ratio and examined the correlation between amino acid variants and two social phenotypes. We also analysed gene expression data to explore associations between brain receptor expression and social phenotype variation. Our findings reveal that, while most sites in nonapeptide receptors are under strong purifying selection, a few sites - primarily in the extended intracellular loop 3 (IL3) of VTR2A receptors - show signatures of positive selection. Additionally, a specific amino acid in VTR2Aa correlates with pair-bonding, suggesting its potential role in social attachment. Together, our results provide new insights into the evolution of the nonapeptide system and its contribution to social diversity in cichlids.

Transposable elements hitchhike on Starships across fungal genomes

2025-06-24

Hanne Griem-Krey , Julia de Fraga Sant’Ana , Ursula Oggenfuss +6 more | bioRxiv (Cold Spring Harbor Laboratory)

Horizontal transfer (HT) of transposable elements (TEs) is a widespread phenomenon in eukaryotes and is often associated with bursts of TE activity. This process profoundly influences genome evolution by introducing … Horizontal transfer (HT) of transposable elements (TEs) is a widespread phenomenon in eukaryotes and is often associated with bursts of TE activity. This process profoundly influences genome evolution by introducing novel genetic material and driving genetic variation. However, the precise mechanisms facilitating these transfers remain largely uncharacterized. Here, we report a recent TE burst in the insect-pathogenic fungus Metarhizium anisopliae . Our analysis reveals that the actively transposing TEs were introduced via hitchhiking on a so-called Starship - a class of large, themselves horizontally transferable transposons found within the fungal subphylum Pezizomycotina . This particular Starship carried 73 TEs, 43 of which exhibited increased copy numbers in the recipient genome, including 508 perfect copies. This expansion triggered extensive structural reshuffling across all chromosomes and led to the formation of a novel chromosome. Remarkably, this structural reorganization was associated with a dramatic phenotypic shift: the loss of pathogenicity. Expanding our analysis to other fungi, we found that Starship-mediated horizontal transfer of TEs is a general phenomenon. A majority (74%) of 618 published Starships also harbor TEs, which can constitute up to 72% of their content. Moreover, Starships serve as sources of actively transposing TEs: 16% of Starships carried at least one TE with a perfect copy found elsewhere in the genome, and identical TEs were observed on Starships from different species. Collectively, our results establish Starships as major vectors of horizontal TE transfer within Pezizomycotina and further highlight their profound impact on recipient fungal genomes through TE piggybacking.

Author Correction: A two-step mechanism for epigenetic specification of centromere identity and function

2025-06-23

Daniele Fachinetti , H. Diego Folco , Yael Nechemia‐Arbely +7 more | Nature Cell Biology

Characterization of Polyploid Embryoid Lines Induced via Unfertilized Ovule Culture of Loquat (Eriobotrya japonica Lindl.)

2025-06-23

Shuming Wang , Tingting Ruan , Yin Zhang +7 more | Horticulturae

Polyploidy plays a significant role in loquat breeding, particularly in triploid breeding for seedless fruit production. Currently, loquat polyploid breeding primarily relies on natural seedling selection and sexual hybridization approaches. … Polyploidy plays a significant role in loquat breeding, particularly in triploid breeding for seedless fruit production. Currently, loquat polyploid breeding primarily relies on natural seedling selection and sexual hybridization approaches. In this study, unfertilized ovules from four loquat varieties were in vitro cultured. Gynogenesis and embryoid regeneration were achieved in ‘Xingning 1’ and ‘Huabai 1’, with ‘Xingning 1’ demonstrating the highest gynogenesis efficiency (21.63%). Flow cytometry and chromosome counting revealed that the obtained embryoid lines included haploid, diploid, tetraploid, hexaploid, and chimeric ploidy types. Further characterization of ‘Xingning 1’-derived embryoid lines through SSR markers and whole-genome resequencing confirmed that the haploid, diploid, tetraploid, and hexaploidy embryoid originated from haploid–somatic chimeras, diploid, doubled diploid and tripled diploid, respectively. Metabolic analysis showed a positive correlation between ploidy level and the content of both soluble sugars and organic acids. This study explored a novel platform for polyploid induction in loquat and may provide methodological insights for improvement of other perennial fruit trees.

The chloroplast genome of the allotriploid, Paeonia × lemoinei cv. Oukan, and its phylogenetic implications

2025-06-23

Mingyang Hao , Jiang Wu , Mengyao Wang +6 more | Mitochondrial DNA Part B

The chloroplast genome of Paeonia × lemoinei cv. Oukan, a newly identified allotriploid from Paeonia sect. Moutan, shows typical tree peony features in size, structure, and gene content. A maximum-likelihood … The chloroplast genome of Paeonia × lemoinei cv. Oukan, a newly identified allotriploid from Paeonia sect. Moutan, shows typical tree peony features in size, structure, and gene content. A maximum-likelihood phylogenetic analysis revealed cv. Oukan and the known triploid cv. Shouanhong clustered into subsect. Delavayanae and subsect. Vaginatae, respectively. Cv. Oukan is closely related to its maternal parent cv. High Noon, while autotriploid cv. Shouanhong is sister to P. ostii but genetically distinct. This study provides genomic resources and phylogenetic insights for the first allotriploid tree peony, suggesting lineages in both subsects could serve as maternal parents for breeding triploid cultivars.

<scp>HELQ</scp> Maintains Genome Stability of Primordial Germ Cells by Inhibiting <scp>LINE</scp>‐1 Expression

2025-06-21

Lili Cao , Jiayi Ren , Zining Kong +6 more | The FASEB Journal

ABSTRACT The DNA helicase HELQ is involved in homologous recombination repair, interstrand cross‐link repair, and replication stress response. Its functional defects are associated with infertility and abnormal gametogenesis. However, the … ABSTRACT The DNA helicase HELQ is involved in homologous recombination repair, interstrand cross‐link repair, and replication stress response. Its functional defects are associated with infertility and abnormal gametogenesis. However, the specific mechanisms of HELQ in the development of germ cells remain to be elucidated. Here, we uncovered that HELQ deficiency led to proliferation defects of primordial germ cells (PGCs) in mouse embryos, thus compromising the establishment of reproductive reserve. Mechanistically, we found that HELQ interacted with the H3K9me3 demethylase KDM4B, and the absence of HELQ led to a marked increase in both total and chromatin‐bound protein levels of KDM4B, resulting in reduced H3K9me3 levels in the region of the retrotransposon LINE‐1, which triggered its high expression and subsequently caused DNA damage accumulation. Moreover, the developmental defects of HELQ‐deficient PGCs were alleviated by inhibition of retrotransposition. These results indicate that HELQ maintains the genome stability of PGCs by repressing LINE‐1 expression. Our study reveals a critical role of HELQ in PGC development and provides new insights into reproductive disorders caused by defects in DNA damage response factors.

piRNA-Mediated Maintenance of Genome Stability in Gametogenesis and Cancer

2025-06-20

Martyna Zawalska , Maciej Tarnowski | Genes

Epigenetics and genome science have become central to current molecular biology research. Among the key mechanisms ensuring genomic integrity is the silencing of transposable elements in germline cells, a process … Epigenetics and genome science have become central to current molecular biology research. Among the key mechanisms ensuring genomic integrity is the silencing of transposable elements in germline cells, a process essential for fertility in both sexes. A pivotal component of this silencing machinery involves PIWI-interacting RNAs (piRNAs), a distinct class of small non-coding RNAs that regulate gene expression and suppress transposable elements at both the transcriptional and post-transcriptional levels. piRNAs function in concert with PIWI proteins, whose expression is critical for proper oogenesis, spermatogenesis, and early zygote development. Disruptions in piRNA or PIWI protein pathways not only impair germline function but also contribute to genome instability, unchecked cell proliferation, and aberrant epigenetic modifications, hallmarks of tumorigenesis. Emerging evidence links the dysregulation of the piRNA/PIWI axis to the development and progression of various cancers, including lung and colorectal carcinomas. This review highlights the fundamental roles of piRNAs and PIWI proteins in reproductive biology and their increasingly recognized relevance in cancer biology.

GAG Protein of Arabidopsis thaliana LTR Retrotransposon Forms Retrosome-like Cytoplasmic Granules and Activates Stress Response Genes

2025-06-20

Alexander Polkhovskiy , Р. А. Комахин , Ilya Kirov | Plants

LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, … LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, we present a comprehensive analysis of the structural features, intracellular localization, and transcriptomic effects of the EVD GAG (evdGAG) protein. Using AlphaFold3, we identified canonical capsid (CA-NTD and CA-CTD) and nucleocapsid (NC) domains, with predicted disordered regions likely facilitating oligomerization. Transient expression of GFP-tagged evdGAG in protoplasts of A. thaliana and distant plant species (Nicotiana benthamiana and Helianthus annuus) revealed the formation of multiple large cytoplasmic aggregates resembling retrosomes, often localized near the nucleus. Stable overexpression of evdGAG in wild-type and ddm1 mutant backgrounds induced significant transcriptomic changes, including up-regulation of stress response and defense-related genes and downregulation of photosynthesis and chloroplast-associated pathways. Importantly, genes linked to stress granule formation were also up-regulated, suggesting a role for evdGAG in modulating cellular stress responses. Our findings provide novel insights into the cellular and molecular properties of plant retrotransposon GAG proteins and their influence on host gene expression.

Efficient induction of parthenogenetic haploids in African marigold (Tagetes erecta) L.) using Co60 gamma-irradiated pollen of French Marigold (Tagetes patula L.)

2025-06-19

Eram Arzoo , Kavita Dubey , Rashmi Arora +7 more | Research Square (Research Square)

<title>Abstract</title> Haploids and doubled haploids play a crucial role in crop improvement programs, including hybridisation, mutation breeding, and genetic and genomic studies. Induction of parthenogenesis using gamma-irradiated pollens is an … <title>Abstract</title> Haploids and doubled haploids play a crucial role in crop improvement programs, including hybridisation, mutation breeding, and genetic and genomic studies. Induction of parthenogenesis using gamma-irradiated pollens is an efficient approach for inducing haploids and developing homozygous lines in horticultural crops. However, no research has been conducted using the induced parthenogenesis approach for haploid induction in the genus Tagetes. This study aims to assess the effectiveness of gamma irradiation at doses of 100, 200, 300, 400, and 500 Gy, using a Co60 (Cobalt-60) source, for haploid induction. The irradiated pollen of a distant tetraploid species, Tagetes patula genotype ‘Pusa Deep’, was used to induce haploids in the diploid marigold species, T. erecta genotypes ‘DAMH-24’ and ‘DAMH-55’. The pseudo-fertilized ovaries were cultured on modified MS medium supplemented with 0.75 mgl-1 TDZ, 0.2 mgl-1 NAA, and 0.5 mgl-1 GA3. To better understand the effect of γ irradiation doses on haploid induction rate, a correlation analysis was performed. Out of 50 regenerants, 20 were selected to determine ploidy levels using morphological traits, chloroplast count, chromosomal count, and flow cytometry analysis. A plant with 3-7 chloroplasts in stomatal guard cells, 2n=x=12 chromosomes, and 1C DNA (~54K mean Pi) was identified as haploid; the plant with 10-14 chloroplasts, 2n=2x=24 chromosomes, and 2C DNA (~108K mean Pi) was diploid, while the plant with 16-20 chloroplasts, 2n=2x=24 chromosomes, and 3C DNA (~154K mean Pi) was triploid. For efficient pollen inactivation and high-throughput haploid induction in Tagetes erecta, the 400 Gy treatment was found to be the most effective.

First karyotype description of Epiplatys spilargyreius (Duméril, 1861) with comments on chromosome evolution in the genus Epiplatys Gill, 1862 (Nothobranchiidae)

2025-06-19

Sergey A. Simanovsky , Alexandra Yu. Skuratovskaya , Margarita G. Simonian +3 more | Comparative Cytogenetics

The African non-annual killifish genus Epiplatys Gill, 1862 (family Nothobranchiidae) comprises 36 valid species distributed in West, Central and East Africa. The available cytogenetic information for the genus indicates a … The African non-annual killifish genus Epiplatys Gill, 1862 (family Nothobranchiidae) comprises 36 valid species distributed in West, Central and East Africa. The available cytogenetic information for the genus indicates a wide variability in diploid chromosome number (2n) and number of chromosome arms (FN). Here, we report the karyotype of Epiplatys spilargyreius (Duméril, 1861), one of the two species with the lowest diploid chromosome number (2n = 34) in the genus, from the White Nile basin in Ethiopia. Male and female karyotypes contained 18 metacentric/acrocentric and 16 subtelocentric/acrocentric chromosomes. The number of chromosome arms is, respectively, FN = 52. Analysis of karyotype differentiation in the genus allowed us to suggest that the 2n reduction in E. spilargyreius and many other members of the genus Epiplatys is mainly due to Robertsonian translocations (reduction of 2n from 48 to 34 with stable NF = 48–52). We provide an up-to-date summary of cytogenetic data and a brief review of chromosome evolution in the genus.

Single-Cell Transcriptome Patterns of Transposable Elements in Alzheimer’s Disease

2025-06-19

Cali M. McEntee , Thomas J. LaRocca | Molecular Neurobiology

<scp>COmapper</scp>: high‐resolution mapping of meiotic crossovers by long‐read sequencing in Arabidopsis

2025-06-19

Dohwan Byun , Namil Son , Heejin Kim +7 more | New Phytologist

Summary Meiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is … Summary Meiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is shaped by chromatin accessibility and DNA polymorphisms. Genome‐wide crossover maps can be generated in plants by high‐throughput short‐read sequencing or linked‐read sequencing. Here, we use long‐read nanopore sequencing technology to develop a crossover mapping pipeline, COmapper, for high‐resolution mapping of genome‐wide crossovers from pooled DNA of F 1 hybrid pollen and F 2 recombinant seedlings derived from a cross between Arabidopsis thaliana accessions Col and L er . We validate the high accuracy of COmapper by applying nanopore long‐read sequencing to the pooled DNA of Arabidopsis F 2 individuals with crossovers mapped by short‐read sequencing. Using the COmapper, we constructed high‐resolution genomic maps of crossovers using F 1 hybrid pollen and F 2 seedlings in wild‐type (WT) and crossover‐elevated recq4a recq4b mutants, showing results comparable to short‐read sequencing. Crossovers were enriched at gene‐proximal promoters in WT and increased but reshaped by high polymorphism density in recq4a recq4b . We propose that COmapper will be widely applicable for exploring the effects of genetic, epigenetic, and environmental changes on the crossover patterns across diverse plant species.

Transposon persistence and control in germ cells

2025-06-18

Lauren Tracy , ZZ Zhao Zhang | Current Opinion in Genetics & Development

Bimodal centromeres in pentaploid dogroses shed light on their unique meiosis

2025-06-18

Veit Herklotz , Meng Zhang , Thiago Nascimento +7 more | Nature

Abstract Sexual reproduction relies on meiotic chromosome pairing to form bivalents, a process that is complicated in polyploids owing to the presence of multiple subgenomes 1 . Uneven ploidy mostly … Abstract Sexual reproduction relies on meiotic chromosome pairing to form bivalents, a process that is complicated in polyploids owing to the presence of multiple subgenomes 1 . Uneven ploidy mostly results in sterility due to unbalanced chromosome pairing and segregation during meiosis. However, pentaploid dogroses ( Rosa sect. Caninae ; 2 n = 5 x = 35) achieve stable sexual reproduction through a unique mechanism: 14 chromosomes form bivalents and are transmitted biparentally, while the remaining 21 chromosomes are maternally inherited as univalents 2,3 . Despite being studied for over a century, the role of centromeres in this process has remained unclear. Here we analyse haplotype-resolved chromosome-level genome assemblies for three pentaploid dogroses. Subgenome phasing revealed a bivalent-forming subgenome with two highly homozygous chromosome sets and three divergent subgenomes lacking homologous partners, therefore explaining their meiotic behaviour. Comparative analyses of chromosome synteny, phylogenetic relationships and centromere composition indicate that the subgenomes originated from two divergent clades of the genus Rosa . Pollen genome analysis shows that subgenomes from different evolutionary origins form bivalents, supporting multiple origins of dogroses and highlighting variation in subgenome contributions. We reveal that bivalent-forming centromeres are enriched with ATHILA retrotransposons, contrasting with larger tandem-repeat-based centromeres mainly found in univalents. This centromere structural bimodality possibly contributes to univalent drive during female meiosis. Our findings provide insights into the unique reproductive strategies of dogroses, advancing our understanding of genome evolution, centromere diversity and meiotic mechanisms in organisms with asymmetrical inheritance systems.

Correction: Chromosomal level genome assembly of medicinal plant Rosa laevigata

2025-06-18

Rongxiang Zhang , Maohui Wang , Guiyu Zhang +6 more | Scientific Data

Telomere-to-telomere genome assembly of Phoxinus lagowskii

2025-06-18

Yanfeng Zhou , Chunhai Chen , Di‐An Fang +7 more | Scientific Data

Colchicine-induced chromosome doubling in Cinnamomum camphora and its effect on morphological and terpenoid storage structures

2025-06-17

Caihui Chen , Pengzhenni Chen , Zhaoxiang Wu +5 more | Industrial Crops and Products

Binding of heterochromatin protein Rhino to a subset of piRNA clusters depends on a combination of two histone marks

2025-06-17

Abdou Akkouche , Emma Kneuss , Susanne Bornelöv +7 more | Nature Structural & Molecular Biology

Abstract Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements (TEs) and maintain genome integrity. In … Abstract Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements (TEs) and maintain genome integrity. In Drosophila melanogaster germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in TE fragments, via an elaborate machinery centered on the Heterochromatin Protein 1 homolog, Rhino. Although Rhino binds to peptides carrying tri-methylated H3K9 in vitro, it is not fully understood why in vivo only a fraction of H3K9me3-decorated heterochromatin is occupied by Rhino. Recent work revealed that Rhino is recruited to a subset of piRNA clusters by Kipferl. Here we identify a Kipferl-independent mode of Rhino recruitment that, in addition to the previously established role of H3K9me3, also depends on the histone H3 lysine 27 methyltransferase Enhancer of Zeste. At Kipferl-independent sites, we find that Rhino specifically binds to loci marked by both H3K9me3 and H3K27me3 via its chromodomain. Although the exact mechanism of how Rhino binding is influenced by dual histone modifications remains unclear from a structural and biochemical perspective, our work suggests that combinatorial modifications may regulate the specificity of chromatin-binding protein interactions. These findings provide an enhanced understanding of how Rhino targets piRNA source loci, highlighting the sophisticated epigenetic landscape governing TE silencing in Drosophila germ cells.

H3K27me3 expands the epigenetic control of piRNA transcription

2025-06-17

Arantxa M. L. Rojas , Germano Cecere | Nature Structural & Molecular Biology

Interploidy hybridization enhances floral phenotypic diversity of Iris × norrisii tetraploids

2025-06-17

Jiacheng Tang , Liya Ding , Yike Gao +5 more | Research Square (Research Square)

<title>Abstract</title> Interploidy hybridization has been widely utilized in plant breeding and cultivar improvement. In ornamental species, interploidy hybridization between diverse diploid lines and synthetic tetraploids enables the transfer of rich … <title>Abstract</title> Interploidy hybridization has been widely utilized in plant breeding and cultivar improvement. In ornamental species, interploidy hybridization between diverse diploid lines and synthetic tetraploids enables the transfer of rich diploid variation to polyploid backgrounds. Although previously applied in the breeding of Irises and other ornamentals, this approach remains insufficiently explored in synthetic polyploid cultivars. To address the limited floral variation observed in artificial tetraploid lines of <italic>Iris</italic> × <italic>norrisii</italic>, we performed interploidy crosses between tetraploid plants and both diploid and mixoploid lines. Hybrid progenies were evaluated based on floral traits, chromosome counts, and the meiotic behavior of microspore mother cells in parental plants. Crosses using tetraploid plants as female parents yielded tetraploid or near-tetraploid aneuploid progeny, whereas those with diploid female parents produced only diploid offspring. Cytological analysis revealed meiotic abnormalities in both diploid and tetraploid, contributing to the formation of unreduced male gametes. Interploidy hybrids displayed a broader range of perianth colors than control tetraploid crosses, whereas floral morphological variation was similar between the two groups. These findings demonstrate that diploid <italic>I. × norrisii</italic> contributes to the diversification of floral traits in tetraploid lines via the transmission of genetic variation through unreduced male gametes. Interploidy hybridization is a promising approach for enhancing phenotypic diversity in polyploid ornamental breeding.

Spatio-temporal chromosomal arrangements by late-replicating heterochromatin

2025-06-17

Satya Dev Polisetty , Shuvadip Dutta , Rakesh Netha Vadnala +3 more | bioRxiv (Cold Spring Harbor Laboratory)

Centromere clustering orchestrates the three-dimensional genome organization and, in turn, impacts genome stability 1-4 . In this study, we report the principles governing the chromosome-scale architectural changes associated with centromere … Centromere clustering orchestrates the three-dimensional genome organization and, in turn, impacts genome stability 1-4 . In this study, we report the principles governing the chromosome-scale architectural changes associated with centromere clustering and declustering in Cryptococcus neoformans , an opportunistic human fungal pathogen. We demonstrate that centromeres and telomeres in C. neoformans are scattered around the nuclear periphery during interphase G1 , resembling metazoans rather than model budding yeasts. Hi-C data of the synchronised cells reveal centromere and telomere-associated heterochromatic regions are organized as separate compartments at the nuclear periphery, distinct from the euchromatic regions, that eventually shape the global organization of interphase G1 chromosomes. Polymer modeling of the Hi-C data at interphase and anaphase stages strongly supports a global reorganization of chromosomes from the non-Rabl to the Rabl-like chromosomal arrangement. Most strikingly, while centromeres are clustered and replicate early in most yeasts, our sort-seq studies provide evidence that C. neoformans centromeres replicate late during the S-phase. In summary, we uncover yet unknown principles governing the chromosome-scale architecture that link centromere DNA replication timing, spatial centromere positioning, functional compartmentalization of chromosomes, and dynamic changes in the global three-dimensional genome architecture in a species that shared a common ancestor with metazoans more than a billion years ago.

NlAgo3 and NlBiwi are essential for piRNAs biogenesis and female reproduction in Nilaparvata lugens

2025-06-17

Shengli Jing , Jingang Xu , Fang Zheng +7 more | Insect Biochemistry and Molecular Biology

DUE-B Is Dispensable for Early Development and Genome Duplication in Vertebrates.

2025-06-17

Courtney G. Sansam , Emily A. Masser , Duane Goins +1 more | bioRxiv (Cold Spring Harbor Laboratory)

The DNA Unwinding Element-Binding protein (DUE-B) is a Cyclin Dependent Kinase (CDK) and Dbf4-Dependent Kinase (DDK) substrate that has been implicated in the control of DNA replication initiation. Knockdown of … The DNA Unwinding Element-Binding protein (DUE-B) is a Cyclin Dependent Kinase (CDK) and Dbf4-Dependent Kinase (DDK) substrate that has been implicated in the control of DNA replication initiation. Knockdown of DUE-B in HeLa cells perturbs the G1-to-S phase transition and immunodepletion of due-b in Xenopus egg extracts blocks replication initiation. Combined prior evidence has suggested that Due-b may be a vertebrate-specific DNA replication initiation factor. Here, we asked whether due-b was an essential vertebrate gene, and whether it was critical for proper embryonic development in the zebrafish Danio rerio. We have generated due-b mutant zebrafish through genome-editing TALENs that fail to express due-b mRNA or protein. Our mutant zebrafish are viable and survive to adulthood. They do not display outward developmental phenotypes, and when stressed with replication inhibitors, do not differ from their wild-type counterparts. Cell cycle analysis demonstrates the DNA replication occurs normally. Our data indicate that Due-b is not a core essential component of the DNA replication initiation machinery required for vertebrate development. Instead, it may be a mechanistically redundant protein or play a specialized role in DNA replication control.

Monkeyflower (Mimulus) uncovers the evolutionary basis of the eukaryote telomere sequence variation

2025-06-16

Surbhi Kumawat , Askhan Shametov , Liia R. Valeeva +7 more | PLoS Genetics

Telomeres are nucleoprotein complexes with crucial role of protecting chromosome ends. Because of its vital functions, components of the telomere, including its sequence, should be under strong evolutionary constraint. Yet … Telomeres are nucleoprotein complexes with crucial role of protecting chromosome ends. Because of its vital functions, components of the telomere, including its sequence, should be under strong evolutionary constraint. Yet across the tree of life there are numerous examples of telomere sequence variation and the evolutionary mechanism driving this diversification is unclear. Here, we studied the telomeres in Mimulus by investigating the noncoding telomerase RNA (TR), which is a core component of the telomere maintenance complex and determines the telomere sequence in eukaryotes. We conducted de novo transcriptomics and genome analysis of 18 species, and discovered Mimulus has evolved at least three different telomere sequences: (AAACCCT) n , (AAACCCG) n , and (AAACCG) n . We discovered several species with TR duplications, implying functional consequences that could influence telomere evolution. For instance, M. lewisii harbored two sequence-divergent TR paralogs while its sister species the paralog had pseudogenized. Nanopore-sequencing and fluorescence in situ hybridization indicated M. lewisii had a sequence heterogeneous telomere, and Telomeric Repeat Amplification Protocol combined with Terminal Restriction Fragment analysis confirmed the telomerase can use both TR paralogs for telomere synthesis. Interestingly in closely related species M. cardinalis , TR was also duplicated and both paralogs were expressed but its telomere consisted of a single telomere repeat. Evolutionary analysis indicated the TR paralogs arose from an ancient duplication, which also underlies the evolutionary origin of multiple Mimulus species with divergent telomere sequences. We propose sequence variation in eukaryotic telomeres arises from an evolutionary process involving TR duplication, sequence divergence, and loss of TR paralog.

Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species

2025-06-16

Zewen Wang , Yunqi Zhang , Xuming Chen +7 more | Planta

The Density of Recombination-Associated Genomic Features Does Not Generally Explain the Broad-Scale Crossover Patterns in Chicken and Guinea Fowl

2025-06-14

Luis Francisco Rossi , M.I. Pigozzi | Animals

Meiotic recombination is essential for chromosomal segregation and facilitates the exchange between homologs, which leads to the transmission of new combinations of linked alleles to the progeny. The eukaryotic meiotic … Meiotic recombination is essential for chromosomal segregation and facilitates the exchange between homologs, which leads to the transmission of new combinations of linked alleles to the progeny. The eukaryotic meiotic machinery is generally highly conserved, but the frequency of crossover occurrence can vary dramatically across species and populations, between individuals, and across sexes. The chicken and the guinea fowl exhibit interspecific variation in the distribution of crossovers along their largest chromosomes. In many organisms, an association has been observed between the preferred crossover location and certain sequence parameters, such as high GC content, CpG islands, or gene promoters. Here, we compared the distribution of these genomic parameters with the recombination landscape, represented by MLH1 focus frequencies, in the two birds. We found an association between GC content density and recombination in the chicken, but the remaining parameters showed weak or no association with recombination, especially in the guinea fowl. We conclude that despite the different broad-scale crossover distribution, the investigated genomic parameters remained remarkably similar in these two species. We suggest that the density of these genomic features is more likely related to microscale variations in recombination rates, such as those determined by open chromatin configurations.

Multiple copy number variants of VC1 gene reveal single-copy expression as a key determinant of vicine content

2025-06-13

Samson Ugwuanyi , Manar H. Makhoul , Agnieszka A. Golicz +2 more | Frontiers in Plant Science

Faba bean is a valuable legume crop desired globally for its high nutritional composition. However, the seed vicine and convicine (v-c) content reduces the nutritional quality of faba bean protein … Faba bean is a valuable legume crop desired globally for its high nutritional composition. However, the seed vicine and convicine (v-c) content reduces the nutritional quality of faba bean protein and can induce favism in susceptible individuals. Recently, VC1 gene, encoding a bi-functional riboflavin protein, was reported to initiate the v-c biosynthetic pathway in V. faba . In low v-c cultivars, a 2 bp insertion in this gene disrupts its function by causing a frameshift and premature stop codon. However, because v-c biosynthesis is only partially reduced, this suggests that additional genes may also be involved in the pathway. Here, we identify and investigate multiple tandem gene duplications at the VC1 locus. Our findings reveal that VC1 exhibits multiple structural variants and copy number variations, but its expression is independent of copy number. Low v-c genotypes carry both variants of the gene — with and without the 2 bp insertion — but only the variant with the insertion is expressed. In contrast, high v-c genotypes consistently express the variant lacking the insertion. Although some high v-c genotypes also carry the insertion, it is found in a non-expressed variant, while the expressed variant lacks the insertion, resulting in the high v-c phenotype. We also report a novel diverging VC1 homolog, RIBA2 , which shares expression domains with VC1 . This homologous gene encodes GTP cyclohydrolase II, a critical enzyme in the v-c pathway. Expression of this gene contributes ~5-10% of riboflavin gene transcripts in immature seeds suggesting it as a minor-effect candidate locus in v-c biosynthesis. Moreover, two SNPs within the coding sequence of RIBA2 segregated with v-c content, offering a reliable alternative for marker-assisted selection in faba bean breeding. In conclusion, this study contributes to the elucidation of the complex genetic regulation of v-c biosynthesis and provides valuable insights to facilitate further efforts in its reduction in faba bean.

Simultaneous editing of SPO11‐1, REC8 and OSD1 yields aneutetraploid soybeans

2025-06-13

Jing Wang , Kejian Wang , Wei‐Cai Yang +1 more | Plant Biotechnology Journal

MORC2 directs transcription-dependent CpG methylation of human LINE-1 transposons in early neurodevelopment

2025-06-13

Fereshteh Dorazehi , Caterina Francesconi , Ninoslav Pandiloski +7 more | bioRxiv (Cold Spring Harbor Laboratory)

Methylation of CpG dinucleotides is essential for silencing genomic repeats such as LINE-1 retrotransposons (L1s) in the germline and soma. Evolutionarily-young L1s are transcribed in human pluripotent stem cells, but … Methylation of CpG dinucleotides is essential for silencing genomic repeats such as LINE-1 retrotransposons (L1s) in the germline and soma. Evolutionarily-young L1s are transcribed in human pluripotent stem cells, but how CpG methylation is patterned to these L1s upon exit of pluripotency is unknown. Here we investigate the critical functions of chromatin regulator MORC2 in epigenome reprogramming of the repetitive genome in early human neurodevelopment. We find that reversible ATP-dependent dimerization is required for MORC2 accumulation over L1s but not gene promoters. Mutation of the MORC2 ATPase module, causative for neurodevelopmental disorders, severely disrupts the distribution of MORC2 chromatin binding, leading to simultaneous loss of L1 transcriptional control and hyper-repression of clustered ZNF genes in human pluripotent stem cells. Upon neural differentiation these phenotypes persist due to striking, targeted defects in CpG methylation patterning. Together our results define the vital role of MORC2 in safeguarding the somatic human genome upon exit of pluripotency by directing CpG methylation patterning over transcriptionally-active retrotransposons in a manner analogous to the piRNA pathway in the germline.

1389-P: Comparative Impact of T1D or T2D and Hyperglycemia on DNA Methylation in Circulating White Cells

2025-06-13

HETAL SHAH , Jonathan M. Dreyfuss , BERKCAN OZTURK +4 more | Diabetes

Introduction and Objective: DNA methylation (DNAm) has been implicated in “metabolic memory” of hyperglycemia and diabetes complication risk. Due to potential reversibility, epigenetic dysregulation may be targeted for therapy. We … Introduction and Objective: DNA methylation (DNAm) has been implicated in “metabolic memory” of hyperglycemia and diabetes complication risk. Due to potential reversibility, epigenetic dysregulation may be targeted for therapy. We aimed to identify DNAm associated with type 1 (T1D) or type 2 (T2D) diabetes vs. non-diabetic individuals (NDM), and the impact of poor glycemic control in these groups. Methods: Buffy coat samples from people with long-duration T1D (Joslin Medalist Study, n=59), T2D (Joslin Heart Study, n=59), and respective age-matched NDM controls (n=46) were used for DNAm analysis (Illumina Methylation EPIC v2.0 935K). Samples were selected from those with poor (HbA1c ≥9%) and good (&lt;7%) glycemic control (1:1 ratio). Using R/Bioconductor, per-probe differential DNAm between groups was determined, adjusting for age, sex, and white blood cell (WBC) type proportions. Results: T1D and T2D groups had mean age 64 years, 64% and 33% females, respectively, and diabetes duration 56 and 14 years. Compared to NDM, T1D had lower BMI (25 kg/m2) and better lipids, while T2D had higher BMI (34 kg/m2) and lipids. No differences in DNAm were observed between HbA1c strata in T1D or T2D. However, significant differences in DNAm were observed in T1D (23K CpGs) and, to a lesser extent, in T2D (298 CpGs) vs. NDM (FDR&lt;0.05). In both T1D and T2D, the majority of differentially methylated sites had decreased DNAm. Differentially methylated probes were enriched (FDR&lt;0.001) in transcription start sites (TSS) and quiescent sites in T1D vs controls, with similar TSS enrichment in T2D. Conclusion: Hyperglycemia (captured by HbA1c) was not associated with significant DNAm differences in WBCs of people with diabetes. However, significant differences in DNAm at TSS were observed in T1D and, to a lesser extent, in T2D. Further studies are needed to understand whether these differences are related to diabetes treatment, disease duration, autoimmunity (T1D), or insulin resistance (T2D). Disclosure H. Shah: None. J. Dreyfuss: None. B. Ozturk: None. R. Ferraz-Bannitz: None. G.L. King: None. A. Doria: Research Support; Abbott, Lexicon Pharmaceuticals, Inc, Dexcom, Inc. M. Patti: Research Support; Dexcom, Inc. Other Relationship; Recordati, Fractyl Health, Inc. Consultant; Spruce Biosciences, Premier, Cello, Alpha sight, Boxer Capital. Other Relationship; Amylyx. Funding Beth Israel Lahey Health (BILH) Epigenetics Initiative

Localization of rDNA-associated retrotransposons refines the heterochromatin map of the X chromosome in Drosophila melanogaster

2025-06-12

Т. Д. Колесникова , О.Ф. Веселова , Galina V. Pokholkova +2 more | Cytogenetic and Genome Research

Introduction: R1 and R2 retrotransposons specifically integrate into 28S rRNA genes, thereby disrupting many rDNA units within the nucleolar organizer region (NOR) of Drosophila. However, they also appear to play … Introduction: R1 and R2 retrotransposons specifically integrate into 28S rRNA genes, thereby disrupting many rDNA units within the nucleolar organizer region (NOR) of Drosophila. However, they also appear to play mutualistic roles, contributing to the maintenance of rDNA copy number and the regulation of nucleolar dominance. In addition to their presence in nucleolar rDNA, R1 elements are strongly enriched in the pericentromeric heterochromatin of the X chromosome, located distal to the NOR. This enrichment coincides with several enigmatic genetic phenomena—such as the ABO and cr phenotypes—whose molecular basis remains poorly understood. Notably, this region is one of the least characterized domains of the D. melanogaster genome, lying outside the reference assembly and unresolved in metaphase chromosome preparations. Methods: We performed cytological mapping of R1 and R2 retrotransposons in D. melanogaster heterochromatin using polytene chromosomes from Rif11 mutant, which suppresses under-replication of all types of heterochromatic sequences. These were combined with classical eu–heterochromatic inversions of the X chromosome. Results and conclusions: We identified distinct clusters of both R1 and R2 elements within the X chromosome heterochromatin outside the NOR. R1 elements are highly enriched in the region between the heterochromatic Stellate (hSte) gene cluster and the NOR. This zone exhibits a unique response to Su(var)3-9 mutations, characterized by pronounced decondensation and the formation of a pseudo-puff. Proximal to the R1-enriched domain and adjacent to hSte cluster, we observed a region enriched in R2 elements. The edges of the NOR also show R2 enrichment, likely corresponding to intra-nucleolar domains that accumulate transcriptionally inactive rDNA units. In contrast, nucleolar R1 elements—which also mark inactive rDNA units—are more evenly distributed across the entire NOR. Based on these findings, we propose a refined cytological map of X chromosome heterochromatin in D. melanogaster.

Whole-genome duplication leads to significant but inconsistent changes in climatic niche

2025-06-12

Patrick G. Meirmans , Filip Kolář | Proceedings of the National Academy of Sciences

Polyploidization (whole-genome duplication, WGD) is a widespread large-effect macromutation with far-reaching genomic, phenotypic, and evolutionary consequences. Yet, we do not know whether the consistent phenotypic changes that are associated with … Polyploidization (whole-genome duplication, WGD) is a widespread large-effect macromutation with far-reaching genomic, phenotypic, and evolutionary consequences. Yet, we do not know whether the consistent phenotypic changes that are associated with polyploidization translate into predictable changes in ecological preferences. Niche modeling studies in mixed-ploidy species provide an opportunity to compare recently originated polyploids with their lower-ploidy ancestors. However, the available isolated studies provide contrasting results and the diverse methodologies used limit generalization. Based on 25,857 georeferenced ploidy-verified occurrence data for 129 mixed-ploidy flowering plant species, we tested in a unified statistical framework whether WGD is associated with consistent changes in climatic niche and in past, current, and predicted future range size. We found that 74% of species exhibited significant niche shifts associated with ploidy transition. However, there was no consistent environmental parameter underlying ploidy differentiation across species, nor was there consistent support for polyploid range or niche expansion in a subset of 75 densely sampled species with sufficient data for modeling. Our results demonstrate that polyploidization is an important factor affecting niche evolution of a species, but the environmental parameters underlying the ploidy-related niche shifts vary from species to species, demonstrating limited predictability of the outcomes of WGD in ecological space.

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution

2025-06-12

Jae Hak Son , Matthew A. Lawlor , Mahek Virani +3 more | bioRxiv (Cold Spring Harbor Laboratory)

Abstract The Drosophila telomere is one of the best-studied examples of active transposable elements (TEs) benefitting, rather than harming, a host genome. All Drosophila species lack telomerase and instead have … Abstract The Drosophila telomere is one of the best-studied examples of active transposable elements (TEs) benefitting, rather than harming, a host genome. All Drosophila species lack telomerase and instead have telomeres composed of head-to-tail arrays of specialized retrotransposons. These TEs ostensibly act as mutualists by elongating chromosome ends, but evidence from species closely related to Drosophila melanogaster suggests that telomeric transposons may also antagonize their host genome. Importantly, the limited number of Drosophila species characterized thus far has precluded our ability to delineate idiosyncratic from universal evolutionary forces and genetic mechanisms that shape the history of these TEs. Here, we have surveyed long-read genome assemblies of over 100 species of Drosophila , identifying a total of 396 telomeric TE families. Our findings show that these telomere-specialized elements evolve rapidly and also undergo striking convergent evolution: the complete loss of telomeric TEs has occurred repeatedly across the genus while individual telomeric TE lineages have repeatedly lost one of their two protein-coding genes. These elements have also repeatedly undergone horizontal transfer between distantly related Drosophila lineages and have repeatedly captured host gene fragments that promote their selfish suppression of host TE-silencing systems. Furthermore, telomere specialization itself appears to have evolved convergently, as some non-telomeric families have gained the ability to target their insertions to telomeres. These results provide unprecedented resolution into the evolution of these unusual TEs and highlight several novel mechanisms by which they evolve in conflict both with each other and their host genome despite the essential telomere function they provide.