Eukaryote DIRS1-like retrotransposons: an overview
<p>Abstract</p> <p>Background</p> <p>DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about th...
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| Format: | Article |
| Language: | English |
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BMC
2011-12-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/12/621 |
| _version_ | 1811329139981942784 |
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| author | Piednoël Mathieu Gonçalves Isabelle R Higuet Dominique Bonnivard Eric |
| author_facet | Piednoël Mathieu Gonçalves Isabelle R Higuet Dominique Bonnivard Eric |
| author_sort | Piednoël Mathieu |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes.</p> <p>Results</p> <p>To determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as <it>Danio rerio </it>and <it>Saccoglossus kowalevskii</it>.</p> <p>Conclusion</p> <p>In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes.</p> |
| first_indexed | 2024-04-13T15:38:33Z |
| format | Article |
| id | doaj.art-357d1dc50ee146c5a4d1de14081667eb |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T15:38:33Z |
| publishDate | 2011-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-357d1dc50ee146c5a4d1de14081667eb2022-12-22T02:41:12ZengBMCBMC Genomics1471-21642011-12-0112162110.1186/1471-2164-12-621Eukaryote DIRS1-like retrotransposons: an overviewPiednoël MathieuGonçalves Isabelle RHiguet DominiqueBonnivard Eric<p>Abstract</p> <p>Background</p> <p>DIRS1-like elements compose one superfamily of tyrosine recombinase-encoding retrotransposons. They have been previously reported in only a few diverse eukaryote species, describing a patchy distribution, and little is known about their origin and dynamics. Recently, we have shown that these retrotransposons are common among decapods, which calls into question the distribution of DIRS1-like retrotransposons among eukaryotes.</p> <p>Results</p> <p>To determine the distribution of DIRS1-like retrotransposons, we developed a new computational tool, ReDoSt, which allows us to identify well-conserved DIRS1-like elements. By screening 274 completely sequenced genomes, we identified more than 4000 DIRS1-like copies distributed among 30 diverse species which can be clustered into roughly 300 families. While the diversity in most species appears restricted to a low copy number, a few bursts of transposition are strongly suggested in certain species, such as <it>Danio rerio </it>and <it>Saccoglossus kowalevskii</it>.</p> <p>Conclusion</p> <p>In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes.</p>http://www.biomedcentral.com/1471-2164/12/621 |
| spellingShingle | Piednoël Mathieu Gonçalves Isabelle R Higuet Dominique Bonnivard Eric Eukaryote DIRS1-like retrotransposons: an overview BMC Genomics |
| title | Eukaryote DIRS1-like retrotransposons: an overview |
| title_full | Eukaryote DIRS1-like retrotransposons: an overview |
| title_fullStr | Eukaryote DIRS1-like retrotransposons: an overview |
| title_full_unstemmed | Eukaryote DIRS1-like retrotransposons: an overview |
| title_short | Eukaryote DIRS1-like retrotransposons: an overview |
| title_sort | eukaryote dirs1 like retrotransposons an overview |
| url | http://www.biomedcentral.com/1471-2164/12/621 |
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