Reverse transcriptase survey

A hidden Markov model (HMM) approach was used to survey the predicted rotifer proteomes for proteins encoding the reverse transcriptase (RT) domain (Pfam ID PF00078). First, a HMM was constructed from an alignment of 51 RT domains from across the tree of life (Arkhipova et al., 2003), supplemented with 67 bdelloid-specific retroelements (Arkhipova et al., 2003; Flot et al., 2013; Gladyshev et al., 2007; Gladyshev and Arkhipova, 2010b; Gladyshev and Arkhipova, 2009; Gladyshev and Arkhipova, 2007). Alternative transcripts were first removed from predicted proteomes and proteins with a significant match (E-value ≤1e−5) were identified and inserted into the core RT alignment using HMMER v3.2.1 ‘hmmsearch’ and ‘hmmalign’, respectively (http://hmmer.org/). Maximum likelihood phylogenies were then constructed using IQ-TREE as above, specifying the root of the phylogeny to be on the branch leading to the bacterial retrons (Arkhipova et al., 2003). Trees were manipulated using FigTree v1.4.4 (Rambaut, 2007), colouring the identified RT-encoding rotifer proteins based on their phylogenetic position.