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 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/).

Keywords: LTR-retrotransposons; Polyprotein domains; Primer binding site; RepeatExplorer; Transposable elements.

Fig. 1

a-b Plots of pairwise genetic distances calculated from multiple sequence alignments of individual protein domains of Ty1/copia (a) and Ty3/gypsy (b) elements. Note that individual polyprotein domains differ considerably in their divergence and that the genetic distances of INT, RT and RH domains in Ty3/gypsy elements have bimodal distributions. The genetic distances were calculated in the program SeaView using observed distance analysis [97]

Fig. 2

Phylogenetic trees and classification of Ty3/gypsy elements. a Unrooted phylogenetic tree inferred from concatenated RT-RH-INT sequences from both Viridiplantae and non-Viridiplantae elements. Branches of elements from non-Viridiplantae species are in gray. Circles, triangles and diamonds mark elements possessing CHD, CHDCR and aRH domain, respectively. Note the different position of aRH domain in the polyprotein of Tat elements. b Collapsed rectangular phylogram inferred from concatenated RT-RH-INT sequences from the Viridiplantae elements. Phylogenetic trees were calculated using maximum likelihood. Trees inferred from the concatenated RT-RH-INT domains were consistent with trees inferred from individual domains (Additional file 6 and data not shown). The only exception included a few chromovirus elements from Selaginella moellendorffii which occurred at discordant positions in the trees. Branches containing these elements are marked with numbers 1, 2, and 3 and were labeled as unclassified chromoviruses. c Proposed classification of Ty3/gypsy elements in plants

Fig. 3

Phylogenetic trees of Ty1/copia elements. Trees were calculated using maximum-likelihood from alignments of protein sequences of concatenated INT-RT-RH (a), INT (b), RT (c) and RH domains (d). Radial phylograms on the left were inferred from datasets containing sequences of both Viridiplantae and non-Viridiplantae elements. Collapsed rectangular phylograms on the right were inferred from data sets containing only sequences from Viridiplantae species. Branches containing elements from non-Viridiplantae species are in gray. Note the discrepancies among individual trees and the relationship of some Ty1/copia groups to non-Viridiplantae elements (branches labeled with circles and names) suggesting that evolution of Ty1/copia may have involved recombination as well as horizontal transfer. All trees were rooted using the Osser clade

Fig. 4

Distribution and characteristic features of individual groups of Ty3/gypsy (a) and Ty1/copia (b) retrotransposons in plants. Question mark in the “PBS type” column denotes similarity to 3′ end of undetermined types of tRNA. PBSs complementary to half-molecule tRNA are designated with a “1/2” prefix before the tRNA type. PBSs exploiting self-priming are labeled as “self”. Prevailing organization of the polyprotein coding ORFs was not determined (labeled ND) in some groups due to random stop codon and frameshift mutations in most elements. All schemes of representative elements are to scale