DOI: 10.5061/dryad.vhhmgqnvf
title: Multiple sequence alignments and phylogenetic trees from: Co-option of the limb patterning program in cephalopod eye development

description: Background Across the Metazoa, similar genetic programs are found in the
 development of analogous, independently evolved, morphological features.
 The functional significance of this reuse and the underlying mechanisms of
 co-option remain unclear. Cephalopods have evolved a highly acute visual
 system with a cup shaped retina and a novel refractive lens in the
 anterior, important for a number of sophisticated behaviors including
 predation, mating and camouflage. Almost nothing is known about the
 molecular-genetics of lens development in the cephalopod. Results Here we
 identify the co-option of the canonical bilaterian limb pattering program
 during cephalopod lens development, a functionally unrelated structure. We
 show radial expression of transcription factors SP6-9/sp1, Dlx/dll,
 Pbx/exd, Meis/hth, and a Prdl homolog in the squid Doryteuthis pealeii,
 similar to expression required in Drosophila limb development. We assess
 the role of Wnt signaling in the cephalopod lens, a positive regulator in
 the developing Drosophila limb, and find the regulatory relationship
 reversed, with ectopic Wnt signaling leading to lens loss. Conclusion This
 regulatory divergence suggests that duplication of SP6-9 in cephalopods
 may mediate the co-option of the limb patterning program. Thus our study
 suggests that the limb network could perform a more universal
 developmental function in radial pattering and highlights how canonical
 genetic programs are repurposed in novel structures.
description: Genes were preliminarily identified using reciprocal BLAST with
 <i>Mus musculus </i>and <i>Drosophila melanogaster
 </i>sequences<i> </i>as bait with the exception of
 S-Crystallin where previous <i>Doryteuthis opalescens
 </i>sequences were also used (Altschul et al., 1990). Top hits in
 the <i>D. pealeii </i>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 <i>D. pealeii
 </i>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).
description: Supplemental Data
 Files: RAxML Maximum Likelihood
 trees, 1000 bootstraps. ANTP_ML_1000bs_final.nex Axin_ML_1000bs_final.nex Cry_ML_1000bs_final.nex Dach_ML_1000bs_final.nex Dsh_ML_1000bs_final.nex Fz_ML_1000bs_final.nex GSK3_ML_1000bs_final.nex Lhx_ML_1000bs_final.nex LRP1_ML_1000bs_final.nex Pangolin_ML_1000bs_final.nex Prd_domain_ML_1000bs_final.nex TALE_ML_1000bs_final.nex Wnt_ML_1000bs_final.nex MAFFT sequence alignments ANTP_ML_1000bs_final.fasta Axin_ML_1000bs_final.fasta Cry_ML_1000bs_final.fasta Dach_ML_1000bs_final.fasta Dsh_ML_1000bs_final.fasta Fz_ML_1000bs_final.fasta GSK3_ML_1000bs_final.fasta Lhx_ML_1000bs_final.fasta LRP1_ML_1000bs_final.fasta Pangolin_ML_1000bs_final.fasta Prd_domain_ML_1000bs_final.fasta TALE_ML_1000bs_final.fasta Wnt_ML_1000bs_final.fasta