Computational protocol: Evolution of the insect Sox genes

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Protocol publication

[…] SOX homologues were identified in insect genome sequences using tBlastN searches []. Each putative AmSOX protein was analysed for the presence of a sequence motif RPMNAFMVW located within the HMG box which is conserved for all SOX sequences [], confirming that those genes identified were members of the SOX group of HMG domain transcription factors. Multiple alignments of honeybee SOX HMG sequences with SOX domains from other species were carried out in ClustalX (see Additional files , and ). For Figure the multiple alignment was analysed using MrBAYES 3.1.2.[] under the WAG model[] with default priors. The WAG model was chosen as the most appropriate model of amino-acid substitution after preliminary analysis using MrBAYES with mixed models. The Monte Carlo Markov Chain search was run with four chains over 1500000 generations with trees sampled every 1000 generations. The first 375000 trees were discarded as 'burn-in'. The trees in figures and were constructed using the PHYLIP[] package of programs from alignments bootstrapped using SEQBOOT. Maximum Likelihood trees were estimated using PROTML and majority-rule consensus trees derived using CONSENSE. Dendrograms were displayed using TreeViewPPC [] or Dendroscope [].Genome sequence information for insects and other species was retrieved from their genome project websites [[,-] and []]. Exon/intron gene structure was predicted by either Genemachine [] or was already predicted during the genome assembly using sets of reference sequences (including Drosophila) to help identify transcripts. Insect Sox genes were named based on their placement within each SOX groups (see Additional file for Genebank accession numbers). […]

Pipeline specifications

Software tools TBLASTN, Clustal W, MrBayes, PHYLIP, Dendroscope
Applications Phylogenetics, Amino acid sequence alignment
Organisms Mus musculus, Homo sapiens, Drosophila melanogaster, Apis mellifera, Nasonia vitripennis, Tribolium castaneum, Anopheles gambiae