Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development
Koenig, Kristen (2021), Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development, Dryad, Dataset, https://doi.org/10.5061/dryad.vhhmgqnvf
Genes were preliminarily identified using reciprocal BLAST with Mus musculus and Drosophila melanogaster sequences as bait with the exception of S-Crystallin where previous Doryteuthis opalescens sequences were also used (Altschul et al., 1990). Top hits in the D. pealeii transcriptome were trimmed for coding sequence and translated to amino acid sequences. To find related sequences, BLASTp was used, searching only the RefSeq protein database in NCBI filtered for vertebrate and arthropod models, as well as spiralian models when published annotated sequences could be found. The top hits of each gene name were downloaded and aligned with D. pealeii sequences for each tree using MAFFT in Geneious (Katoh, 2002). To check sequence redundancy and proper outgroups quick trees were made using FastTree. We constructed maximum-likelihood trees on the FASRC Cannon cluster supported by the FAS Division of Science Research Computing Group at Harvard University (Price et al. 2010). Using PTHREADS RAxML v.8.2.10, we ran the option for rapid bootstrapping with searcxh for best maximum likelihood tree, resampling with 1000 bootstrap replicates, the PROTGAMMAAUTO model of amino acid substitution, and otherwise default parameters (Stamatakis, 2014).
Supplemental Data Files:
RAxML Maximum Likelihood trees, 1000 bootstraps.
MAFFT sequence alignments
NIH Office of the Director, Award: 1DP5OD023111-01