LTR retrotransposons in fungi.
Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fung...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22242120/?tool=EBI |
| _version_ | 1818722502647480320 |
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| author | Anna Muszewska Marta Hoffman-Sommer Marcin Grynberg |
| author_facet | Anna Muszewska Marta Hoffman-Sommer Marcin Grynberg |
| author_sort | Anna Muszewska |
| collection | DOAJ |
| description | Transposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other. |
| first_indexed | 2024-12-17T20:55:39Z |
| format | Article |
| id | doaj.art-05806d40a9f344e292f23aed9b944721 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T20:55:39Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-05806d40a9f344e292f23aed9b9447212022-12-21T21:32:52ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01612e2942510.1371/journal.pone.0029425LTR retrotransposons in fungi.Anna MuszewskaMarta Hoffman-SommerMarcin GrynbergTransposable elements with long terminal direct repeats (LTR TEs) are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (<50 elements), others demonstrate huge expansions (>8000 elements). The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22242120/?tool=EBI |
| spellingShingle | Anna Muszewska Marta Hoffman-Sommer Marcin Grynberg LTR retrotransposons in fungi. PLoS ONE |
| title | LTR retrotransposons in fungi. |
| title_full | LTR retrotransposons in fungi. |
| title_fullStr | LTR retrotransposons in fungi. |
| title_full_unstemmed | LTR retrotransposons in fungi. |
| title_short | LTR retrotransposons in fungi. |
| title_sort | ltr retrotransposons in fungi |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22242120/?tool=EBI |
| work_keys_str_mv | AT annamuszewska ltrretrotransposonsinfungi AT martahoffmansommer ltrretrotransposonsinfungi AT marcingrynberg ltrretrotransposonsinfungi |