Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F19%3A00511288" target="_blank" >RIV/60077344:_____/19:00511288 - isvavai.cz</a>

Result on the web

<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0144-1" target="_blank" >https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0144-1</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13100-018-0144-1" target="_blank" >10.1186/s13100-018-0144-1</a>

Result language

angličtina

Original language name

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Original language description

BackgroundPlant 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.ResultsWe 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.ConclusionsWe 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/).

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10603 - Genetics and heredity (medical genetics to be 3)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2019

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Mobile DNA

ISSN

1759-8753

e-ISSN

—

Volume of the periodical

10

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

17

Pages from-to

1

UT code for WoS article

000454930500001

EID of the result in the Scopus database

2-s2.0-85059632655