Functional annotation, enrichment, and clustering

The functional annotation of transcripts was based on the Trinotate pipeline (version 3.0.1). We matched microarray probe sequences to known sequences using BLAST against the SwissProt annotated database (Apweiler et al., 2004), identified protein sequence homology using HMMER and Pfam (Finn, Clements & Eddy, 2011; Finn et al., 2015), and searched for known annotations within eggNOG and GO databases (The Gene Ontology Consortium, 2015; Huerta-Cepas et al., 2016). Ontology enrichment was determined using GOSeq (version 3.4, Young et al., 2010), a statistical package for R which accounts for multiple testing as well as differing probe lengths. Finally, clustering of gene modules was performed using the WGCNA package for R (version 1.51, Langfelder & Horvath, 2008) with a minimum module size of five genes.