Protein-coding genes were aligned in frame, as per the alignment conducted for the phylogenetic analysis.
Phylogenetic analyses of the CLTC alignment, conducted to provide an estimate of the CLTC gene tree, used RAxML 7.0.4 [ 37].
EJ participated in sequence acquisition and alignment, conducted phylogenetic analyses and drafted the MS. GG participated in DNA sequence acquisition and analyses.
DH participated in the genome sequence alignment, conducted the quality control of the assembled raw data and added helpful ideas to the manuscript.
Sequence alignments conducted by JTM and MJM and data analyses were undertaken by MJM.
We base this assessment on local TBA multisequence alignments conducted between entire rainbow trout and Atlantic salmon BAC clone assemblies.
In addition to whole-peptide alignments, this predicted effect on peptide structure was also observed in structural alignments conducted using only residues on the 5′-end of the peptide (residues −16 to −12).
However we could not construct a reasonable alignment to conduct phylogenetic analyses, because sequence similarity was evident only in a limited region.
After manual inspection and editing where necessary, sequences were aligned using ClustalX [33]; the intron alignment was conducted by taking into account secondary structure following Goddard and Burt [6].
Sequence alignment was conducted with BLAST tools provided by the National Center for Biotechnology Information.
Alignment was conducted using ClustalW within MEGA6 (Tamura et al. 2013), gap opening penalty 5; gap extension penalty 1.5 was set for both pairwise and multiple alignments.
