Journal Article

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

Neumann, Pavel, Novák, Petr, Hoštáková, Nina, Macas, Jiří

2019

Overview

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/ ).

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Anopheles / Binding sites / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Classification / Deoxyribonucleic acid / Developmental Biology / DNA / Family relations / Flowers & plants / Genomes / Genomics / Human Genetics / LTR-retrotransposons / Microbial Genetics and Genomics / Microbiology / Phylogenetics / Phylogeny / Plant genetics / Plant Genetics and Genomics / Polyprotein domains / Primer binding site / Proteins / RepeatExplorer / Software / Transfer RNA / Transposable elements / Transposons / Web sites (World Wide Web)