Figure 1.
The diversity of tyrosine recombinase elements (YREs) and their diagnostic features for taxonomic classification.
The known taxonomic distribution of each element (A–H) is listed along with a cartoon of its structure. Metazoa are in bold font and Ecdysozoa are underlined. The features considered are the presence and absence of the reverse transcriptase (RT), methyltransferase (MT) and tyrosine recombinase (YR) domains and their orientation (grey triangles), as well as the presence, absence and position of split direct repeats (pairs of triangles, sharing a colour and pointing in the same orientation), inverted repeats (pairs of triangles, sharing a colour and pointing in opposite orientation) and zinc finger motifs from the Gag protein. Where a question mark is indicated, some members of the group possess and others lack a zinc finger motif.
Figure 2.
Schematic description of the workflow utilized in this study.
A flow chart of the analysis steps described in the Material and Methods section, including the homology searches for YRE protein domains, the classification of YREs based on their features, the phylogenetic reconstruction of YRE relationships and their phylogenetic classification.
Table 1.
Mean contig lengths, contig length at N50 and PSIBLASTN putative transposable element counts of the genomes analysed.
Figure 3.
The distribution of YREs among Nematoda and outgroup species.
The phylogenetic tree of Nematoda is based on De Ley and Blaxter [47] and Kiontke et al. [48]. Element types are colour coded. The phylogenetically classified YRE matches in each species are indicated. Pie-charts represent the proportion of each element type with their radii proportional to the number of phylogenetically classified YRE matches.
Figure 4.
The phylogenetic relationships among YREs recovered from Nematoda and outgroup species.
The phylogeny of the YREs was derived from analyses of the RT domains (A) and the YR domains (B). Character state changes of diagnostic YRE features are indicated as follows: YR: tyrosine recombinase domains; DR: split direct repeats; IR: inverted repeats; I: inversion of the YR domain; T: translocation of the internal repeats; zf: zinc finger in the Gag protein. sh - like branch supports are indicated at the base of nodes. Feature based classification, and the inclusion of reference sequences is indicated on each leaf. Where the leaves have a branch support symbol, these leaves are in fact collapsed clades.