Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification
Abstract Background Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related s...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | Mobile DNA |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13100-018-0144-1 |
| _version_ | 1818323182814232576 |
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| author | Pavel Neumann Petr Novák Nina Hoštáková Jiří Macas |
| author_facet | Pavel Neumann Petr Novák Nina Hoštáková Jiří Macas |
| author_sort | Pavel Neumann |
| collection | DOAJ |
| description | Abstract Background Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons. Results We have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains. Conclusions We have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/). |
| first_indexed | 2024-12-13T11:08:38Z |
| format | Article |
| id | doaj.art-3d7b9ae10deb4d11a5ffec2a64b99b64 |
| institution | Directory Open Access Journal |
| issn | 1759-8753 |
| language | English |
| last_indexed | 2024-12-13T11:08:38Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Mobile DNA |
| spelling | doaj.art-3d7b9ae10deb4d11a5ffec2a64b99b642022-12-21T23:48:51ZengBMCMobile DNA1759-87532019-01-0110111710.1186/s13100-018-0144-1Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classificationPavel Neumann0Petr Novák1Nina Hoštáková2Jiří Macas3Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyBiology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyBiology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyBiology Centre of the Czech Academy of Sciences, Institute of Plant Molecular BiologyAbstract Background Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons. Results We have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains. Conclusions We have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/).http://link.springer.com/article/10.1186/s13100-018-0144-1LTR-retrotransposonsTransposable elementsPolyprotein domainsPrimer binding siteRepeatExplorer |
| spellingShingle | Pavel Neumann Petr Novák Nina Hoštáková Jiří Macas Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification Mobile DNA LTR-retrotransposons Transposable elements Polyprotein domains Primer binding site RepeatExplorer |
| title | Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| title_full | Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| title_fullStr | Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| title_full_unstemmed | Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| title_short | Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| title_sort | systematic survey of plant ltr retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification |
| topic | LTR-retrotransposons Transposable elements Polyprotein domains Primer binding site RepeatExplorer |
| url | http://link.springer.com/article/10.1186/s13100-018-0144-1 |
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