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do Nascimento Moreira C, Cardoso AL, Valeri MP, Ventura K, Ferguson-Smith MA, Yonenaga-Yassuda Y, Svartman M, Martins C. Characterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae). Mol Genet Genomics 2023:10.1007/s00438-023-02038-w. [PMID: 37233800 DOI: 10.1007/s00438-023-02038-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Repetitive DNA are sequences repeated hundreds or thousands of times and an abundant part of eukaryotic genomes. SatDNA represents the majority of the repetitive sequences, followed by transposable elements. The species Holochilus nanus (HNA) belongs to the rodent tribe Oryzomyini, the most taxonomically diverse of Sigmodontinae subfamily. Cytogenetic studies on Oryzomyini reflect such diversity by revealing an exceptional range of karyotype variability. However, little is known about the repetitive DNA content and its involvement in chromosomal diversification of these species. In the search for a more detailed understanding about the composition of repetitive DNA on the genome of HNA and other species of Oryzomyini, we employed a combination of bioinformatic, cytogenetic and molecular techniques to characterize the repetitive DNA content of these species. RepeatExplorer analysis showed that almost half of repetitive content of HNA genome are composed by Long Terminal Repeats and a less significant portion are composed by Short Interspersed Nuclear Elements and Long Interspersed Nuclear Elements. RepeatMasker showed that more than 30% of HNA genome are composed by repetitive sequences, with two main waves of repetitive element insertion. It was also possible to identify a satellite DNA sequence present in the centromeric region of Oryzomyini species, and a repetitive sequence enriched on the long arm of HNA X chromosome. Also, comparative analysis between HNA genome with and without B chromosome did not evidence any repeat element enriched on the supernumerary, suggesting that B chromosome of HNA is composed by a fraction of repeats from all the genome.
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Affiliation(s)
- Camila do Nascimento Moreira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
| | - Adauto Lima Cardoso
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Mirela Pelizaro Valeri
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Karen Ventura
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cesar Martins
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Kass DH, Beatty S, Smith A, Scott M, Shah D, Czaplicki M. The discovery of multiple active mys-related LTR-retroelements within the Neotominae subfamily of cricetid rodents. Genetica 2023:10.1007/s10709-023-00183-z. [PMID: 36869995 DOI: 10.1007/s10709-023-00183-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023]
Abstract
Retrotransposon families in the rodent family Cricetidae have been understudied in contrast to Muridae, both taxa classified within the superfamily Muroidea. Therefore, we carried out a study to advance our knowledge of the unique mys LTR-retroelement identified in Peromyscus leucopus, by incorporating intra-ORF PCR, quantitative dot blots, DNA and protein library screens, the generation of molecular phylogenies, and analyses of orthologous LTR-retroelement loci. These analyses led to the discovery of three additional related families of LTR-retroelements, which include a 2900 bp full-length element of mys-related sequences (mysRS), an 8000 bp element containing the mys ORF1 sequence (mORF1) with ERV-related sequences downstream in the reverse orientation, as well as an 1800 bp element primarily consisting of mys ORF2 (mORF2) related sequences flanked by LTRs. Our data revealed only a few full-length mys elements among genera of the Neotominae subfamily of cricetid rodents, most existing as partial copies. The mysRS and mORF1 elements are also limited to the genomes of the Neotominae subfamily, whereas mORF2 appears to be restricted to the Peromyscus genus. Molecular phylogenies demonstrating concerted evolution along with an assessment of orthologous loci in Peromyscus for the presence or absence of elements are consistent with activity of these novel LTR-retroelement families within this genus. Together with known activity of various families of non-LTR retroelements in Peromyscus species, we propose that retrotransposons have been continually contributing to the dynamics of Peromyscus genomes promoting genomic diversity and may be correlated with the evolution of more than 50 identified Peromyscus species.
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Affiliation(s)
- David H Kass
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA.
| | - Sarah Beatty
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Ashlee Smith
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Megan Scott
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Dishita Shah
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Mary Czaplicki
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
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Soares SC, Eler ES, E Silva CEF, da Silva MNF, Araújo NP, Svartman M, Feldberg E. LINE-1 and SINE-B1 mapping and genome diversification in Proechimys species (Rodentia: Echimyidae). Life Sci Alliance 2022; 5:5/6/e202101104. [PMID: 35304430 PMCID: PMC8932440 DOI: 10.26508/lsa.202101104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022] Open
Abstract
This study aimed to understand the impact of LINE-1 and SINE-B1 retroelements on the architecture and karyotypic diversification of five rodent species of the genus Proechimys from different regions of the Amazon. Karyotype comparisons were performed using fluorescent interspecific in situ hybridization. The L1 and B1 retroelements showed a non-random arrangement and a conserved pattern when the genomes of the five species of Proechimys were compared, including the two cytotypes of Proechimys guyannensis The signal homeology among the chromosomes and the degree of similarity among the formed clusters indicate rearrangements such as fusion/fission, and demonstrates that these retroelements can behave as derived characters shared in Proechimys The differentiated distribution and organization of these retroelements in the karyotypes and in the chromosomal fiber, respectively, may represent a strong indication of their role as generating sources of karyotypic diversity in the genus Proechimys and provide insights into the evolutionary relationships between taxa.
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Affiliation(s)
- Simone Cardoso Soares
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil .,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eduardo Schmidt Eler
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carlos Eduardo Faresin E Silva
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | | | - Naiara Pereira Araújo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de Rondônia campus Jaru, Jaru, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eliana Feldberg
- Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.,Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
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Petersen M, Winter S, Coimbra R, J de Jong M, Kapitonov VV, Nilsson MA. Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae. Mob DNA 2021; 12:27. [PMID: 34836553 PMCID: PMC8620236 DOI: 10.1186/s13100-021-00254-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. RESULTS The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. CONCLUSIONS The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.
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Affiliation(s)
- Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108, Freiburg, Germany
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Raphael Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Menno J de Jong
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Vladimir V Kapitonov
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
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Fukuda S, Narendran S, Varshney A, Nagasaka Y, Wang SB, Ambati K, Apicella I, Pereira F, Fowler BJ, Yasuma T, Hirahara S, Yasuma R, Huang P, Yerramothu P, Makin RD, Wang M, Baker KL, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Banerjee D, Bonilha VL, Tolstonog GV, Held U, Ogura Y, Terasaki H, Oshika T, Bhattarai D, Kim KB, Feldman SH, Aguirre JI, Hinton DR, Kerur N, Sadda SR, Schumann GG, Gelfand BD, Ambati J. Alu complementary DNA is enriched in atrophic macular degeneration and triggers retinal pigmented epithelium toxicity via cytosolic innate immunity. SCIENCE ADVANCES 2021; 7:eabj3658. [PMID: 34586848 PMCID: PMC8480932 DOI: 10.1126/sciadv.abj3658] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/05/2021] [Indexed: 05/08/2023]
Abstract
Long interspersed nuclear element-1 (L1)–mediated reverse transcription (RT) of Alu RNA into cytoplasmic Alu complementary DNA (cDNA) has been implicated in retinal pigmented epithelium (RPE) degeneration. The mechanism of Alu cDNA–induced cytotoxicity and its relevance to human disease are unknown. Here we report that Alu cDNA is highly enriched in the RPE of human eyes with geographic atrophy, an untreatable form of age-related macular degeneration. We demonstrate that the DNA sensor cGAS engages Alu cDNA to induce cytosolic mitochondrial DNA escape, which amplifies cGAS activation, triggering RPE degeneration via the inflammasome. The L1-extinct rice rat was resistant to Alu RNA–induced Alu cDNA synthesis and RPE degeneration, which were enabled upon L1-RT overexpression. Nucleoside RT inhibitors (NRTIs), which inhibit both L1-RT and inflammasome activity, and NRTI derivatives (Kamuvudines) that inhibit inflammasome, but not RT, both block Alu cDNA toxicity, identifying inflammasome activation as the terminal effector of RPE degeneration.
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Affiliation(s)
- Shinichi Fukuda
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Siddharth Narendran
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Aravind Eye Hospital System, Madurai, India
| | - Akhil Varshney
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Yosuke Nagasaka
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shao-bin Wang
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kameshwari Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ivana Apicella
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Felipe Pereira
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Benjamin J. Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA
| | - Tetsuhiro Yasuma
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Shuichiro Hirahara
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Reo Yasuma
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Peirong Huang
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Praveen Yerramothu
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Ryan D. Makin
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Mo Wang
- Doheny Eye Institute, Los Angeles, CA, USA
| | | | | | | | - Elmira Baghdasaryan
- Doheny Eye Institute, Los Angeles, CA, USA
- Department of Ophthalmology, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, California, USA
| | - Meenakshi Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Center for Digital Image Evaluation, Charlottesville, VA, USA
| | - Vidya L. Ambati
- Center for Digital Image Evaluation, Charlottesville, VA, USA
| | - Daipayan Banerjee
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Genrich V. Tolstonog
- Department of Otolaryngology–Head and Neck Surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ulrike Held
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Yuichiro Ogura
- Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuro Oshika
- Department of Ophthalmology, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Deepak Bhattarai
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Sanford H. Feldman
- Center for Comparative Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - J. Ignacio Aguirre
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - David R. Hinton
- Departments of Pathology and Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Nagaraj Kerur
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Srinivas R. Sadda
- Doheny Eye Institute, Los Angeles, CA, USA
- Department of Ophthalmology, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, California, USA
| | - Gerald G. Schumann
- Department of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Bradley D. Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
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Araújo NP, Sena RS, Bonvicino CR, Kuhn GCS, Svartman M. SINE-B1 Distribution and Chromosome Rearrangements in the South American Proechimys gr. goeldii (Echimyidae, Rodentia). Cytogenet Genome Res 2021; 161:6-13. [PMID: 33556945 DOI: 10.1159/000513106] [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] [Received: 03/18/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Proechimys species are remarkable for their extensive chromosome rearrangements, representing a good model to understand genome evolution. Herein, we cytogenetically analyzed 3 different cytotypes of Proechimys gr. goeldii to assess their evolutionary relationship. We also mapped the transposable element SINE-B1 on the chromosomes of P. gr. goeldii in order to investigate its distribution among individuals and evaluate its possible contribution to karyotype remodeling in this species. SINE-B1 showed a dispersed distribution along chromosome arms and was also detected at the pericentromeric regions of some chromosomes, including pair 1 and the sex chromosomes, which are involved in chromosome rearrangements. In addition, we describe a new cytotype for P. gr. goeldii, reinforcing the significant role of gross chromosomal rearrangements during the evolution of the genus. The results of FISH with SINE-B1 suggest that this issue should be more deeply investigated for a better understanding of its role in the mechanisms involved in the wide variety of Proechimys karyotypes.
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Affiliation(s)
- Naiara P Araújo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de Rondônia, Jaru, Brazil
| | - Radarane S Sena
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil,
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8
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Yang L, Scott L, Wichman HA. Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mob DNA 2019; 10:22. [PMID: 31139266 PMCID: PMC6530004 DOI: 10.1186/s13100-019-0164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background L1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently compose ~ 20% of a mammalian genome. B1 retrotransposons are dependent on L1 for retrotransposition and span the evolutionary history of rodents since their radiation. L1s were found to have lost their activity in a group of South American rodents, the Sigmodontinae, and B1 inactivation preceded the extinction of L1 in the same group. Consequently, a basal group of sigmodontines have active L1s but inactive B1s and a derived clade have both inactive L1s and B1s. It has been suggested that B1s became extinct during a long period of L1 quiescence and that L1s subsequently reemerged in the basal group. Results Here we investigate the evolutionary histories of L1 and B1 in the sigmodontine rodents and show that L1 activity continued until after the L1-extinct clade and the basal group diverged. After the split, L1 had a small burst of activity in the former group, followed by extinction. In the basal group, activity was initially low but was followed by a dramatic increase in L1 activity. We found the last wave of B1 retrotransposition was large and probably preceded the split between the two rodent clades. Conclusions Given that L1s had been steadily retrotransposing during the time corresponding to B1 extinction and that the burst of B1 activity preceding B1 extinction was large, we conclude that B1 extinction was not a result of L1 quiescence. Rather, the burst of B1 activity may have contributed to L1 extinction both by competition with L1 and by putting strong selective pressure on the host to control retrotransposition. Electronic supplementary material The online version of this article (10.1186/s13100-019-0164-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Yang
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - LuAnn Scott
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - Holly A Wichman
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
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9
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Peçanha WT, Quintela FM, Jorge Ribas LE, Althoff SL, Maestri R, Gonçalves GL, De Freitas TRO. A new species of Oxymycterus (Rodentia: Cricetidae: Sigmodontinae) from a transitional area of Cerrado – Atlantic Forest in southeastern Brazil. J Mammal 2019. [DOI: 10.1093/jmammal/gyz060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Willian Thomaz Peçanha
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501–970, Brazil
| | - Fernando Marques Quintela
- Universidade Federal do Rio Grande, Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais. Av. Itália km 8, Rio Grande, RS, Brazil
| | - Luiz Eduardo Jorge Ribas
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501–970, Brazil
| | - Sérgio Luiz Althoff
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, CEP Blumenau, SC 89012–900, Brazil
| | - Renan Maestri
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501–970, Brazil
| | - Gislene Lopes Gonçalves
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile
| | - Thales R O De Freitas
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501–970, Brazil
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10
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Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev 2018; 49:15-24. [PMID: 29505963 DOI: 10.1016/j.gde.2018.02.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/30/2022]
Abstract
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution.
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11
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Platt RN, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res 2018; 26:25-43. [PMID: 29392473 PMCID: PMC5857283 DOI: 10.1007/s10577-017-9570-z] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/12/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022]
Abstract
Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | | | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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12
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Dodt WG, Gallus S, Phillips MJ, Nilsson MA. Resolving kangaroo phylogeny and overcoming retrotransposon ascertainment bias. Sci Rep 2017; 7:16811. [PMID: 29196678 PMCID: PMC5711953 DOI: 10.1038/s41598-017-16148-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 10/26/2017] [Indexed: 01/31/2023] Open
Abstract
Reconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the genera Macropus and Wallabia. An exhaustive in silico screening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses. We identified robust support for the enigmatic swamp wallaby (Wallabia bicolor) falling within a paraphyletic genus, Macropus. Our statistical approach provides a means to test for incomplete lineage sorting and introgression/hybridization in the presence of the ascertainment bias. Using retrotransposons as “molecular fossils”, we reveal one of the most complex patterns of hemiplasy yet identified, during the rapid diversification of kangaroos and wallabies. Ancestral state reconstruction incorporating the new retrotransposon phylogenetic information reveals multiple independent ecological shifts among kangaroos into more open habitats, coinciding with the Pliocene onset of increased aridification in Australia from ~3.6 million years ago.
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Affiliation(s)
- William G Dodt
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), 2 George Street, Brisbane, Australia.
| | - Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre (BiK-F) Frankfurt, Senckenberg Gesellschaft fuer Naturforschung, Senckenberganlage 25, Frankfurt am Main, Germany
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology (QUT), 2 George Street, Brisbane, Australia.
| | - Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Centre (BiK-F) Frankfurt, Senckenberg Gesellschaft fuer Naturforschung, Senckenberganlage 25, Frankfurt am Main, Germany.
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13
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Comparative Genomic In Situ Hybridization and the Possible Role of Retroelements in the Karyotypic Evolution of Three Akodontini Species. Int J Genomics 2017; 2017:5935380. [PMID: 28900618 PMCID: PMC5576401 DOI: 10.1155/2017/5935380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/14/2017] [Accepted: 05/03/2017] [Indexed: 01/21/2023] Open
Abstract
South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A. montensis (2n = 24, FN = 42), and Necromys lasiurus (2n = 34, FN = 34), after GTG- and CBG-banding. The karyotypes differed by Robertsonian rearrangements, pericentric inversions, centromere repositioning, and heterochromatin variation. Genome comparisons were performed through interspecific fluorescent in situ hybridization (FISH) with total genomic DNAs of each species as probes (GISH). Our results revealed considerable conservation of the euchromatic portions among the three karyotypes suggesting that they mostly differ in their heterochromatic regions. FISH was also performed to assess the distribution of telomeric sequences, long and short interspersed repetitive elements (LINE-1 and B1 SINE) and of the endogenous retrovirus mysTR in the genomes of the three species. The results led us to infer that transposable elements have played an important role in the enormous chromosome variation found in Akodontini.
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14
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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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15
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Gallus S, Lammers F, Nilsson MA. When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials. Genome Biol Evol 2016; 8:2406-12. [PMID: 27389686 PMCID: PMC5010896 DOI: 10.1093/gbe/evw159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads.
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Affiliation(s)
- Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Johann Wolfgang Goethe University Frankfurt Am Main, Max-von-Laue Straβe 9, 60438 Frankfurt am Main, Germany
| | - Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Johann Wolfgang Goethe University Frankfurt Am Main, Max-von-Laue Straβe 9, 60438 Frankfurt am Main, Germany
| | - Maria Anna Nilsson
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung, Senckenberg Anlage 25, Frankfurt, Germany
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16
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Nilsson MA. The devil is in the details: Transposable element analysis of the Tasmanian devil genome. Mob Genet Elements 2015; 6:e1119926. [PMID: 27066301 DOI: 10.1080/2159256x.2015.1119926] [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: 10/06/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022] Open
Abstract
The third marsupial genome was sequenced from the Tasmanian devil (Sarcophilus harrisii), a species that currently is driven to extinction by a rare transmissible cancer. The transposable element (TE) landscape of the Tasmanian devil genome revealed that the main driver of retrotransposition the Long INterspersed Element 1 (LINE1) seem to have become inactivated during the past 12 million years. Strangely, the Short INterspersed Elements (SINE), that normally hijacks the LINE1 retrotransposition system, became inactive prior to LINE1 at around 30 million years ago. The SINE inactivation was in vitro verified in several species. Here I discuss that the apparent LINE1 inactivation might be caused by a genome assembly artifact. The repetitive fraction of any genome is highly complex to assemble and the observed problems are not unique to the Tasmanian devil genome.
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Affiliation(s)
- Maria A Nilsson
- Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung , Frankfurt am Main, Germany
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17
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Gallus S, Hallström BM, Kumar V, Dodt WG, Janke A, Schumann GG, Nilsson MA. Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Mol Biol Evol 2015; 32:1268-83. [PMID: 25633377 PMCID: PMC4408412 DOI: 10.1093/molbev/msv017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
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Affiliation(s)
- Susanne Gallus
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Björn M Hallström
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Vikas Kumar
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - William G Dodt
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Qld, Australia
| | - Axel Janke
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Maria A Nilsson
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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18
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Yang L, Brunsfeld J, Scott L, Wichman H. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 2014; 10:e1004395. [PMID: 24968166 PMCID: PMC4072516 DOI: 10.1371/journal.pgen.1004395] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family, Pteropodidae, ∼24 million years ago. To examine the characteristics of L1s prior to their extinction, we analyzed the evolutionary history of L1s in the genome of a megabat, Pteropus vampyrus, and found a pattern of periodic L1 expansion and quiescence. In contrast to the well-characterized L1s in human and mouse, megabat genomes have accommodated two or more simultaneously active L1 families throughout their evolutionary history, and major peaks of L1 deposition into the genome always involved multiple families. We compared the consensus sequences of the two major megabat L1 families at the time of their extinction to consensus L1s of a variety of mammalian species. Megabat L1s are comparable to the other mammalian L1s in terms of adenosine content and conserved amino acids in the open reading frames (ORFs). However, the intergenic region (IGR) of the reconstructed element from the more active family is dramatically longer than the IGR of well-characterized human and mouse L1s. We synthesized the reconstructed element from this L1 family and tested the ability of its components to support retrotransposition in a tissue culture assay. Both ORFs are capable of supporting retrotransposition, while the IGR is inhibitory to retrotransposition, especially when combined with either of the reconstructed ORFs. We dissected the inhibitory effect of the IGR by testing truncated and shuffled versions and found that length is a key factor, but not the only one affecting inhibition of retrotransposition. Although the IGR is inhibitory to retrotransposition, this inhibition does not account for the extinction of L1s in megabats. Overall, the evolution of the L1 sequence or the quiescence of L1 is unlikely the reason of L1 extinction.
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Affiliation(s)
- Lei Yang
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - John Brunsfeld
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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19
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González-Ittig RE, Rivera PC, Levis SC, Calderón GE, Gardenal CN. The molecular phylogenetics of the genusOligoryzomys(Rodentia: Cricetidae) clarifies rodent host-hantavirus associations. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Raul E. González-Ittig
- Instituto de Diversidad y Ecología Animal (CONICET-UNC); Facultad de Ciencias Exactas, Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Paula C. Rivera
- Instituto de Diversidad y Ecología Animal (CONICET-UNC); Facultad de Ciencias Exactas, Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Silvana C. Levis
- Instituto Nacional de Enfermedades Virales Humanas (INEVH); Pergamino Argentina
| | - Gladys E. Calderón
- Instituto Nacional de Enfermedades Virales Humanas (INEVH); Pergamino Argentina
| | - Cristina N. Gardenal
- Instituto de Diversidad y Ecología Animal (CONICET-UNC); Facultad de Ciencias Exactas, Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
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20
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Wagstaff BJ, Kroutter EN, Derbes RS, Belancio VP, Roy-Engel AM. Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements. Mol Biol Evol 2012; 30:88-99. [PMID: 22918960 PMCID: PMC3525338 DOI: 10.1093/molbev/mss202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Non-long terminal repeat retroelements continue to impact the human genome through
cis-activity of long interspersed element-1 (LINE-1 or L1) and trans-mobilization of Alu.
Current activity is dominated by modern subfamilies of these elements, leaving behind an
evolutionary graveyard of extinct Alu and L1 subfamilies. Because Alu is a nonautonomous
element that relies on L1 to retrotranspose, there is the possibility that competition
between these elements has driven selection and antagonistic coevolution between Alu and
L1. Through analysis of synonymous versus nonsynonymous codon evolution across L1
subfamilies, we find that the C-terminal ORF2 cys domain experienced a dramatic increase
in amino acid substitution rate in the transition from L1PA5 to L1PA4 subfamilies. This
observation coincides with the previously reported rapid evolution of ORF1 during the same
transition period. Ancestral Alu sequences have been previously reconstructed, as their
short size and ubiquity have made it relatively easy to retrieve consensus sequences from
the human genome. In contrast, creating constructs of extinct L1 copies is a more
laborious task. Here, we report our efforts to recreate and evaluate the
retrotransposition capabilities of two ancestral L1 elements, L1PA4 and L1PA8 that were
active ∼18 and ∼40 Ma, respectively. Relative to the modern L1PA1 subfamily, we
find that both elements are similarly active in a cell culture retrotransposition assay in
HeLa, and both are able to efficiently trans-mobilize Alu elements from several
subfamilies. Although we observe some variation in Alu subfamily retrotransposition
efficiency, any coevolution that may have occurred between LINEs and SINEs is not evident
from these data. Population dynamics and stochastic variation in the number of active
source elements likely play an important role in individual LINE or SINE subfamily
amplification. If coevolution also contributes to changing retrotransposition rates and
the progression of subfamilies, cell factors are likely to play an important mediating
role in changing LINE-SINE interactions over evolutionary time.
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Affiliation(s)
- Bradley J Wagstaff
- Department of Epidemiology and Tulane Cancer Center, Tulane University, New Orleans, LA, USA
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21
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Wagstaff BJ, Hedges DJ, Derbes RS, Campos Sanchez R, Chiaromonte F, Makova KD, Roy-Engel AM. Rescuing Alu: recovery of new inserts shows LINE-1 preserves Alu activity through A-tail expansion. PLoS Genet 2012; 8:e1002842. [PMID: 22912586 PMCID: PMC3415434 DOI: 10.1371/journal.pgen.1002842] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 05/30/2012] [Indexed: 12/15/2022] Open
Abstract
Alu elements are trans-mobilized by the autonomous non-LTR retroelement, LINE-1 (L1). Alu-induced insertion mutagenesis contributes to about 0.1% human genetic disease and is responsible for the majority of the documented instances of human retroelement insertion-induced disease. Here we introduce a SINE recovery method that provides a complementary approach for comprehensive analysis of the impact and biological mechanisms of Alu retrotransposition. Using this approach, we recovered 226 de novo tagged Alu inserts in HeLa cells. Our analysis reveals that in human cells marked Alu inserts driven by either exogenously supplied full length L1 or ORF2 protein are indistinguishable. Four percent of de novo Alu inserts were associated with genomic deletions and rearrangements and lacked the hallmarks of retrotransposition. In contrast to L1 inserts, 5′ truncations of Alu inserts are rare, as most of the recovered inserts (96.5%) are full length. De novo Alus show a random pattern of insertion across chromosomes, but further characterization revealed an Alu insertion bias exists favoring insertion near other SINEs, highly conserved elements, with almost 60% landing within genes. De novo Alu inserts show no evidence of RNA editing. Priming for reverse transcription rarely occurred within the first 20 bp (most 5′) of the A-tail. The A-tails of recovered inserts show significant expansion, with many at least doubling in length. Sequence manipulation of the construct led to the demonstration that the A-tail expansion likely occurs during insertion due to slippage by the L1 ORF2 protein. We postulate that the A-tail expansion directly impacts Alu evolution by reintroducing new active source elements to counteract the natural loss of active Alus and minimizing Alu extinction. SINEs are mobile elements that are found ubiquitously throughout a large diversity of genomes from plants to mammals. The human SINE, Alu, is among the most successful mobile elements, with more than one million copies in the genome. Due to its high activity and ability to insert throughout the genome, Alu retrotransposition is responsible for the majority of diseases reported to be caused by mobile element activity. To further evaluate the genomic impact of SINEs, we recovered and characterized over 200 de novo Alu inserts under controlled conditions. Our data reinforce observations on the mutagenic potential of Alu, with newly retrotransposed Alu elements favoring insertion into genic and highly conserved elements. Alu-mediated deletions and rearrangements are infrequent and lack the typical hallmarks of TPRT retrotransposition, suggesting the use of an alternate method for resolving retrotransposition intermediates or an atypical insertion mechanism. Our data also provide novel insights into SINE retrotransposition biology. We found that slippage of L1 ORF2 protein during reverse transcription expands the A-tails of de novo insertions. We propose that the L1 ORF2 protein plays a major role in minimizing Alu extinction by reintroducing active Alu elements to counter the natural loss of Alu source elements.
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Affiliation(s)
- Bradley J. Wagstaff
- Tulane Cancer Center, Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Dale J. Hedges
- Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Rebecca S. Derbes
- Tulane Cancer Center, Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Rebeca Campos Sanchez
- Department of Biology, Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Francesca Chiaromonte
- Department of Biology, Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Department of Biology, Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Astrid M. Roy-Engel
- Tulane Cancer Center, Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
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22
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Platt II RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 2012; 500:47-53. [DOI: 10.1016/j.gene.2012.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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23
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Retrofitting the genome: L1 extinction follows endogenous retroviral expansion in a group of muroid rodents. J Virol 2011; 85:12315-23. [PMID: 21957310 DOI: 10.1128/jvi.05180-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1; L1) retrotransposons are the most common retroelements in mammalian genomes. Unlike individual families of endogenous retroviruses (ERVs), they have remained active throughout the mammalian radiation and are responsible for most of the retroelement movement and much genome rearrangement within mammals. They can be viewed as occupying a substantial niche within mammalian genomes. Our previous demonstration that L1s and B1 short interspersed nuclear elements (SINEs) are inactive in a group of South American rodents led us to ask if other elements have amplified to fill the empty niche. We identified a novel and highly active family of ERVs (mysTR). To determine whether loss of L1 activity was correlated with expansion of mysTR, we examined mysTR activity in four South American rodent species that have lost L1 and B1 activity and four sister species with active L1s. The copy number of recent mysTR insertions was extremely high, with an average of 4,200 copies per genome. High copy numbers exist in both L1-active and L1-extinct species, so the mysTR expansion appears to have preceded the loss of both SINE and L1 activity rather than to have filled an empty niche created by their loss. It may be coincidental that two unusual genomic events--loss of L1 activity and massive expansion of an ERV family--occur in the same group of mammals. Alternatively, it is possible that this large ERV expansion set the stage for L1 extinction.
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González-Ittig RE, Salazar-Bravo J, Barquez RM, Gardenal CN. Phylogenetic relationships among species of the genus Oligoryzomys (Rodentia, Cricetidae) from Central and South America. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00446.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pritham EJ. Transposable elements and factors influencing their success in eukaryotes. J Hered 2009; 100:648-55. [PMID: 19666747 DOI: 10.1093/jhered/esp065] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Recent advances in genome sequencing have led to a vast accumulation of transposable element data. Consideration of the genome sequencing projects in a phylogenetic context reveals that despite the hundreds of eukaryotic genomes that have been sequenced, a strong bias in sampling exists. There is a general under-representation of unicellular eukaryotes and a dearth of genome projects in many branches of the eukaryotic phylogeny. Among sequenced genomes, great variation in genome size exists, however, little difference in the total number of cellular genes is observed. For many eukaryotes, the remaining genomic space is extremely dynamic and predominantly composed of a menagerie of populations of transposable elements. Given the dynamic nature of the genomic niche filled by transposable elements, it is evident that these elements have played an important role in genome evolution. The contribution of transposable elements to genome architecture and to the advent of genetic novelty is likely to be dependent, at least in part, on the transposition mechanism, diversity, number, and rate of turnover of transposable elements in the genome at any given time. The focus of this review is the discussion of some of the forces that act to shape transposable element diversity within and between genomes.
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Affiliation(s)
- Ellen J Pritham
- Department of Biology, University of Texas, Arlington, Arlington, TX 76019, USA.
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Guinea pig ID-like families of SINEs. Gene 2009; 436:23-9. [PMID: 19232383 DOI: 10.1016/j.gene.2009.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 01/29/2009] [Accepted: 02/05/2009] [Indexed: 11/23/2022]
Abstract
Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A-B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents.
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Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 2008; 18:343-58. [PMID: 18256243 DOI: 10.1101/gr.5558208] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from the activity of type I retrotransposons, which amplify in a "copy-and-paste" fashion through an RNA intermediate. For better or worse, the sequences of these retrotransposons are now wedded to the genomes of their mammalian hosts. Although there are several reported instances of the positive contribution of mobile elements to their host genomes, these discoveries have occurred alongside growing evidence of the role of TEs in human disease and genetic instability. Here we examine, with a particular emphasis on human retrotransposon activity, several newly discovered aspects of mammalian retrotransposon biology. We consider their potential impact on host biology as well as their ultimate implications for the nature of the TE-host relationship.
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Affiliation(s)
- Victoria P Belancio
- Tulane Cancer Center and Department of Epidemiology, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA
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Bringaud F, Müller M, Cerqueira GC, Smith M, Rochette A, El-Sayed NMA, Papadopoulou B, Ghedin E. Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania. PLoS Pathog 2007; 3:1291-307. [PMID: 17907803 PMCID: PMC2323293 DOI: 10.1371/journal.ppat.0030136] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 07/27/2007] [Indexed: 01/29/2023] Open
Abstract
Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.
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Affiliation(s)
- Frédéric Bringaud
- Laboratoire de Génomique Fonctionnelle des Trypanosomatides, Université Victor Segalen Bordeaux 2, Bordeaux, France
- UMR-5234 CNRS, Bordeaux, France
| | - Michaela Müller
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Gustavo Coutinho Cerqueira
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Departamento de Bioquimica e Imunologica, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Martin Smith
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Annie Rochette
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Najib M. A El-Sayed
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, The University of Maryland, College Park, Maryland, United States of America
| | - Barbara Papadopoulou
- Infectious Diseases Research Center, Centre Hospitalier de l'Université Laval Research Center, Quebec, Canada
- Department of Medical Biology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Elodie Ghedin
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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Veniaminova NA, Vassetzky NS, Kramerov DA. B1 SINEs in different rodent families. Genomics 2007; 89:678-86. [PMID: 17433864 DOI: 10.1016/j.ygeno.2007.02.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 02/28/2007] [Accepted: 02/28/2007] [Indexed: 11/18/2022]
Abstract
B1 SINEs were studied in 22 families covering all major rodent lineages. The number of B1 copies considerably varies, from 1 x 10(4) in Geomyidae to 1 x 10(6) in Myodonta. B1 sequences can be divided into three main structural variants: B1 with a 20-bp tandem duplication (found in Gliridae, Sciuridae, and Aplodontidae), B1 with a 29-bp duplication (found in other families), and proto-B1 without duplication (pB1). These variants can be further subdivided according to their characters, including specific 7-, 9-, or 10-bp deletions. Different B1 subfamilies predominate in different rodent families. The analysis of B1 variants allowed us to propose possible pathways for the evolution of this SINE in the context of rodent evolution.
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Affiliation(s)
- Natalia A Veniaminova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, Moscow 119991, Russia
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Scott LA, Kuroiwa A, Matsuda Y, Wichman HA. X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO. Cytogenet Genome Res 2006; 112:261-9. [PMID: 16484782 DOI: 10.1159/000089880] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Accepted: 07/25/2005] [Indexed: 01/02/2023] Open
Abstract
The observation that LINE-1 transposable elements are enriched on the X in comparison to the autosomes led to the hypothesis that LINE-1s play a role in X chromosome inactivation. If this hypothesis is correct, loss of LINE-1 activity would be expected to result in species extinction or in an alternate pathway of dosage compensation. One such alternative pathway would be to evolve a karyotype that does not require dosage compensation between the sexes. Two of the three extant species of the Ryukyu spiny rat Tokudaia have such a karyotype; both males and females are XO. We asked whether this karyotype arose due to loss of LINE-1 activity and thus the loss of a putative component in the X inactivation pathway. Although XO Tokudaia has no need for dosage compensation, LINE-1s have been recently active in Tokudaia osimensis and show higher density on the lone X than on the autosomes.
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Affiliation(s)
- L A Scott
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Cantrell MA, Ederer MM, Erickson IK, Swier VJ, Baker RJ, Wichman HA. MysTR: an endogenous retrovirus family in mammals that is undergoing recent amplifications to unprecedented copy numbers. J Virol 2006; 79:14698-707. [PMID: 16282470 PMCID: PMC1287555 DOI: 10.1128/jvi.79.23.14698-14707.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large percentage of the repetitive elements in mammalian genomes are retroelements, which have been moved primarily by LINE-1 retrotransposons and endogenous retroviruses. Although LINE-1 elements have remained active throughout the mammalian radiation, specific groups of endogenous retroviruses generally remain active for comparatively shorter periods of time. Identification of an unusual extinction of LINE-1 activity in a group of South American rodents has opened a window for examination of the interplay in mammalian genomes between these ubiquitous retroelements. In the course of a search for any type of repetitive sequences whose copy numbers have substantially changed in Oryzomys palustris, a species that has lost LINE-1 activity, versus Sigmodon hispidus, a closely related species retaining LINE-1 activity, we have identified an endogenous retrovirus family differentially amplified in these two species. Analysis of three full-length, recently transposed copies, called mysTR elements, revealed gag, pro, and pol coding regions containing stop codons which may have accumulated either before or after retrotransposition. Isolation of related sequences in S. hispidus and the LINE-1 active outgroup species, Peromyscus maniculatus, by PCR of a pro-pol region has allowed determination of copy numbers in each species. Unusually high copy numbers of approximately 10,000 in O. palustris versus 1,000 in S. hispidus and 4,500 in the more distantly related P. maniculatus leave open the question of whether there is a connection between endogenous retrovirus activity and LINE-1 inactivity. Nevertheless, these independent expansions of mysTR represent recent amplifications of this endogenous retrovirus family to unprecedented levels.
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Affiliation(s)
- Michael A Cantrell
- Department of Biological Sciences, PO Box 443051, University of Idaho, Moscow, ID 83844, USA.
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