Bacterial RT phylogeny.

2014-11-25T03:07:58Z (GMT) by Nicolás Toro Rafael Nisa-Martínez
<p>Unrooted phylogenetic trees based on the alignment of the RT-domain (domains 0–7) of the 742 sequences used as the dataset. The group II intron ORF classes and varieties are designated according to the most recent proposals from Toro <i>et al.</i> in 2013 and Simon <i>et al.</i> in 2008 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114083#pone.0114083-Toro3" target="_blank">[28]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114083#pone.0114083-Simon2" target="_blank">[42]</a>. Additional group II intron ORF varieties are also annotated here (<i>g5</i> and <i>g6</i>, see the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114083#s3" target="_blank">results and discussion</a> section). Other RT groups are named as previously reported <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114083#pone.0114083-Simon1" target="_blank">[15]</a> and suggested in this work. (<i>A</i>) A consensus unrooted tree estimated by FastTree method. The main groups were color-coded to improve visualization and collapsed at the internal nodes with local support values ≧0.96, with the exceptions of UG4 (0.84) and UG5 (0.87). Local support values ≧0.95 at inner nodes are also indicated. (<i>B</i>) A consensus unrooted tree estimated by the RAxML method. The main groups were collapsed at the internal nodes with strong support (bootstrap values ≧75%), with the exception of class ML (55%), subgroup CL1B (34%) and variety <i>g3</i> (71%); UG10 (G2L3) (39%); and DGRs (17%). Inner nodes with strong statistical support (bootstrap values ≧80%) are also indicated.</p>