Figure 1.
ORF phylogeny based on alignments of the amino-acid sequences of unclassified and class F intron-encoded ORFs.
(A) Phylogenetic tree based on the X-domain and its C-terminal extension. (B) Phylogenetic tree based on the RT-domain. MLE consensus trees based on MSAs generated with Clustal W, using the WAG substitution model. Trees are rooted at their midpoint. Bootstrap results (≥75%) are given at each node (PhyML) and the rate of amino-acid substitutions per site is shown at the bottom of each tree. Introns assigned to class F are indicated and highlighted in bold typeface.
Figure 2.
Phylogeny of group II intron ORF classes lacking a recognizable D/En region.
(A) Phylogenetic tree based on the alignment of the X-domain and its C-terminal extension. (B) Phylogenetic tree based on the alignment of the RT-domain (0–7). Consensus unrooted trees estimated by ML methods are presented as a radial phylogram. The phylogenetic ORF classes are indicated and the rate of amino-acid substitutions per site is shown at the bottom of each tree. The branches of the major classes are also color-coded to improve visualization of the major clades. Bootstrap results (≥75%) are given for each node (PhyML). Posterior probability values (≥0.96) for Bayesian analysis of the major phylogenetic ORF classes are also indicated in italics. Introns previously classified as phylogenetic ORF class F are indicated by an asterisk.
Figure 3.
RT domain-based phylogeny of group II intron ORFs.
To the MSA alignment used for Fig. 2B, representatives of classes B: En.fmI3, B.a.I2, En.fm.I1, E.f.I3, B.me.I1, C.d.I1, G.k.I1, and B.c.I5; CL1A: A.v.I1, P.p.I2, E.c.I5, Th.e.I1, B.t.I1, Sh.sp.I1, Ms.b.I1; CL1B: B.me.I2, and B.a.I1; CL2A: Tr.e.I2, G.v.I1, Ns.p.I4, Cs.p.I1, and C.w.I1; CL2B: C.w.I6, Ns.p.I2, and Ns.p.I1; and ML: Ba.fr.I1, B.t.I2, N.a.I2, and L.l.I1 used by Simon et al. [15] were added (RT 0–7). The corresponding accession numbers can be obtained from the bacterial group II intron database. A consensus unrooted tree is shown and major ORF classes and the new groups are labeled. Bootstrap results (≥75%) are given for each node (PhyML). The arrow indicates the common node of the lineage of group II introns with an En domain in their IEPs. The circle indicates the possible node grouping together class F introns.