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Cavin L, Alvarez N. Why Coelacanths Are Almost “Living Fossils”? Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.896111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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2
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Xiao SJ, Mou ZB, Yang RB, Fan DD, Liu JQ, Zou Y, Zhu SL, Zou M, Zhou CW, Liu HP. Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau. Zool Res 2021; 42:502-513. [PMID: 34254744 PMCID: PMC8317186 DOI: 10.24272/j.issn.2095-8137.2021.096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Persistent uplift means the Qinghai-Tibet Plateau (QTP) is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments. However, how paleogeographic and paleoclimatic events influence the genome and population of endemic fish species remains unclear. Glyptosternon maculatum is an ancient endemic fish found on the QTP and the only critically endangered species in the Sisoridae family. Here, we found that major transposons in the G. maculatum genome showed episodic bursts, consistent with contemporaneous geological and climatic events during the QTP formation. Notably, histone genes showed significant expansion in the G. maculatum genome, which may be mediated by long interspersed nuclear elements (LINE) repetitive element duplications. Population analysis showed that ancestral G. maculatum populations experienced two significant depressions 2.6 million years ago (Mya) and 10 000 years ago, exhibiting excellent synchronization with Quaternary glaciation and the Younger Dryas, respectively. Thus, we propose that paleogeography and paleoclimate were dominating driving forces for population dynamics in endemic fish on the QTP. Tectonic movements and temperature fluctuation likely destroyed the habitat and disrupted the drainage connectivity among populations. These factors may have caused severe bottlenecks and limited migration among ancestral G. maculatum populations, resulting in the low genetic diversity and endangered status of the species today.
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Affiliation(s)
- Shi-Jun Xiao
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 810000, China.,Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China.,College of Plant Protection, Jilin Agriculture University, Changchun, Jilin 130118, China.,Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, Zhejiang 314000, China
| | - Zen-Bo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 810000, China
| | - Rui-Bin Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ding-Ding Fan
- College of Fisheries, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jia-Qi Liu
- Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Yu Zou
- Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Shi-Lin Zhu
- Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Ming Zou
- Department of Computer Science, Wuhan University of Technology, Wuhan, Hubei 430070, China
| | - Chao-Wei Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 810000, China.,Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 402400, China. E-mail:
| | - Hai-Ping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 810000, China. E-mail:
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3
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Gao B, Sang Y, Zong W, Diaby M, Shen D, Wang S, Wang Y, Chen C, Song C. Evolution and domestication of Tc1/mariner transposons in the genome of African coelacanth ( Latimeria chalumnae). Genome 2020; 63:375-386. [PMID: 32268072 DOI: 10.1139/gen-2019-0216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Here, we comprehensively analysed the abundance, diversity, and activity of Tc1/mariner transposons in African coelacanth (Latimeria chalumnae). Fifteen Tc1/mariner autonomous transposons were identified and grouped into six clades: DD34E/Tc1, DD34D/mariner, DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger, belonging to three known families: DD34E/Tc1, DD34D/mariner, and DD×D/pogo (DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger). Thirty-one miniature inverted-repeat transposable element (MITE) transposons of Tc1/mariner were also identified, and 20 of them display similarity to the identified autonomous transposons. The structural organization of these full Tc1/mariner elements includes a transposase gene flanked by terminal inverted repeats (TIRs) with TA dinucleotides. The transposases contain N-terminal DNA binding domain and a C-terminal catalytic domain characterized by the presence of a conservative D(Asp)DE(Glu)/D triad that is essential for transposase activity. The Tc1/mariner superfamily in coelacanth exhibited very low genome coverage (0.3%), but it experienced an extraordinary difference of proliferation dynamics among the six clades identified; moreover, most of them exhibited a very recent and current proliferation, suggesting that some copies of these transposons are putatively active. Additionally, at least four functional genes derived from Tc1/mariner transposons were found. We provide an up-to-date overview of Tc1/mariner in coelacanth, which may be helpful in determining genome and gene evolution in this living fossil.
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Affiliation(s)
- Bo Gao
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yatong Sang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Wencheng Zong
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Mohamed Diaby
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Dan Shen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Saisai Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yali Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Chengyi Song
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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4
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Lee H, Zhang Z, Krause HM. Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners? Trends Genet 2019; 35:892-902. [PMID: 31662190 DOI: 10.1016/j.tig.2019.09.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/22/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022]
Abstract
Our recent ability to sequence entire genomes, along with all of their transcribed RNAs, has led to the surprising finding that only ∼1% of the human genome is used to encode proteins. This finding has led to vigorous debate over the functional importance of the transcribed but untranslated portions of the genome. Currently, scientists tend to assume coding genes are functional until proven not to be, while the opposite is true for noncoding genes. This review takes a new look at the evidence for and against widespread noncoding gene functionality. We focus in particular on long noncoding RNA (noncoding RNAs longer than 200 nucleotides) genes and their 'junk' associates, transposable elements, and satellite repeats. Taken together, the suggestion put forward is that more of this junk DNA may be functional than nonfunctional and that noncoding RNAs and transposable elements act symbiotically to drive evolution.
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Affiliation(s)
- Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Henry M Krause
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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Makhrov AA. Decreased Evolutionary Plasticity as a Result of Phylogenetic Immobilization and Its Ecological Significance. CONTEMP PROBL ECOL+ 2019. [DOI: 10.1134/s199542551905007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Wong WY, Simakov O. RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation. Bioinformatics 2019; 35:1051-1052. [PMID: 30165587 PMCID: PMC6419915 DOI: 10.1093/bioinformatics/bty745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/27/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022] Open
Abstract
SUMMARY Repetitive elements comprise large proportion of many genomes. They have impact on both genome evolution and regulation. Their classification and the study of evolutionary history is a major emerging field. Various software exist to-date to classify and map repeats across genomes. The major unresolved drawback, however, is the fragmented nature of many identified repeat loci. This ultimately makes the classification of novel repeats and their evolutionary analyses difficult. To improve on this, we developed a pipeline (RepeatCraft) that integrates results from several repeat element classification tools based on both sequence similarity and structural features. The pipeline de-fragments closely spaced repeat loci in the genomes, reconstructing longer copies, thus allowing for a better annotation and sequence comparisons. The pipeline also includes a user interface that can run in a web browser allowing for an easy access and exploration of the repeat data. AVAILABILITY AND IMPLEMENTATION RepeatCraft is implemented in Python and the web application is implemented in R. Download and documentation is freely available at https://github.com/niccw/repeatCraftp. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wai Yee Wong
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
| | - Oleg Simakov
- Department of Molecular Evolution and Development, Faculty of Life Science, University of Vienna, A-1090 Vienna, Austria
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7
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Coan RLB, Martins C. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. Genes (Basel) 2018; 9:genes9060269. [PMID: 29882892 PMCID: PMC6027319 DOI: 10.3390/genes9060269] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022] Open
Abstract
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.
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Affiliation(s)
- Rafael L B Coan
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
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Luchetti A, Plazzi F, Mantovani B. Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth. Genome Biol Evol 2017; 9:3824762. [PMID: 28505260 PMCID: PMC5499810 DOI: 10.1093/gbe/evx094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/11/2022] Open
Abstract
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3′-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Federico Plazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
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9
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Biscotti MA, Canapa A, Forkoni M, Gerdol M, Pallavicini A, Schartl M, Barucca M. The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family. Genome Biol Evol 2017; 9:438-453. [PMID: 28206606 PMCID: PMC5381642 DOI: 10.1093/gbe/evx017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 12/21/2016] [Accepted: 02/04/2017] [Indexed: 12/20/2022] Open
Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Mariko Forkoni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università di Trieste (Italy)
| | | | - Manifred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg and Comprehensive Cancer Center Mainfranken, University Clinic Wuerzburg, Wuerzburg, Germany; and Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona (Italy)
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Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 2017; 9:161-177. [PMID: 28158585 PMCID: PMC5381603 DOI: 10.1093/gbe/evw264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.
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Affiliation(s)
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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Abstract
Retrotransposons carrying tyrosine recombinases (YR) are widespread in eukaryotes. The first described tyrosine recombinase mobile element, DIRS1, is a retroelement from the slime mold Dictyostelium discoideum. The YR elements are bordered by terminal repeats related to their replication via free circular dsDNA intermediates. Site-specific recombination is believed to integrate the circle without creating duplications of the target sites. Recently a large number of YR retrotransposons have been described, including elements from fungi (mucorales and basidiomycetes), plants (green algae) and a wide range of animals including nematodes, insects, sea urchins, fish, amphibia and reptiles. YR retrotransposons can be divided into three major groups: the DIRS elements, PAT-like and the Ngaro elements. The three groups form distinct clades on phylogenetic trees based on alignments of reverse transcriptase/ribonuclease H (RT/RH) and YR sequences, and also having some structural distinctions. A group of eukaryote DNA transposons, cryptons, also carry tyrosine recombinases. These DNA transposons do not encode a reverse transcriptase. They have been detected in several pathogenic fungi and oomycetes. Sequence comparisons suggest that the crypton YRs are related to those of the YR retrotransposons. We suggest that the YR retrotransposons arose from the combination of a crypton-like YR DNA transposon and the RT/RH encoding sequence of a retrotransposon. This acquisition must have occurred at a very early point in the evolution of eukaryotes.
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12
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Naville M, Chalopin D, Casane D, Laurenti P, Volff JN. The coelacanth: Can a "living fossil" have active transposable elements in its genome? Mob Genet Elements 2015; 5:55-59. [PMID: 26442185 DOI: 10.1080/2159256x.2015.1052184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 01/24/2023] Open
Abstract
The coelacanth has long been regarded as a "living fossil," with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a "living fossil." Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a "non-fossil" vertebrate species.
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Affiliation(s)
- Magali Naville
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Domitille Chalopin
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Didier Casane
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Patrick Laurenti
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Jean-Nicolas Volff
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
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13
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Chalopin D, Naville M, Plard F, Galiana D, Volff JN. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol Evol 2015; 7:567-80. [PMID: 25577199 PMCID: PMC4350176 DOI: 10.1093/gbe/evv005] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.
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Affiliation(s)
- Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Floriane Plard
- Laboratoire "Biométrie et Biologie Évolutive," Unité Mixte de Recherche 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard Lyon 1, Lyon Cedex 07, France
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14
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Naville M, Chalopin D, Volff JN. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths. PLoS One 2014; 9:e114382. [PMID: 25470617 PMCID: PMC4255032 DOI: 10.1371/journal.pone.0114382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/10/2014] [Indexed: 01/29/2023] Open
Abstract
Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.
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Affiliation(s)
- Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
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15
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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16
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Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics 2014; 197:625-41. [PMID: 24700104 PMCID: PMC4063920 DOI: 10.1534/genetics.114.164293] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 03/20/2014] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.
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Affiliation(s)
- Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Indrajit Nanda
- Institute of Human Genetics, University of Würzburg, D-97074 Würzburg, Germany
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Ron Walter
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, 97074 Würzburg, Germany
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17
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Forconi M, Chalopin D, Barucca M, Biscotti MA, De Moro G, Galiana D, Gerdol M, Pallavicini A, Canapa A, Olmo E, Volff JN. Transcriptional activity of transposable elements in coelacanth. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:379-89. [PMID: 24038780 DOI: 10.1002/jez.b.22527] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 07/14/2013] [Indexed: 01/22/2023]
Abstract
The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity.
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Affiliation(s)
- Mariko Forconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy; Institut de Génomique Fonctionnelle de Lyon, ENS Lyon, France
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