This is a repository containing all of the code used to generate the manuscript "Evolution of gene expression across species and specialized zooids in Siphonophora".
In this manuscript, we investigate the differential gene expression patterns between distinct zooid types, as well as in a specialized tissue (the pneumatophore). Manuscript code, as well as many of the datafiles needed to complete the analyses, can be found here. However, some of the larger files are hosted on figshare: orthofinder gene trees and results (10.6084/m9.figshare.14838384), strict orthologs (10.6084/m9.figshare.14838372), the json file containing the expression data (10.6084/m9.figshare.14829183), protein sequences for each species (10.6084/m9.figshare.14838090), and the sqlite file that is generated by Agalma 2.0 (10.6084/m9.figshare.14838315). Raw sequence data and associated sampling metadata can be found on NCBI (BioProject ID PRJNA540747).
Analyses start with the script Manuscript_prep. This outputs an RData file that is read in by the script ancestral_trait_recon, which in turn outputs an RData file that is read in by the main manuscript Rmd file. Many of the functions used in analyses are kept in a functions file.
A small blast analysis of Physalia toxins can be found here, and Wnt genes, based on supplementary data from Condamine et al., 2019, can be found here.
