Transcriptome Assembly
We trimmed RNA-seq raw reads for adapters with BBDuk
(https://sourceforge.net/projects/bbmap/) (k = 17, tpe option), and used
STAR 2.7.3a (Dobin et al., 2013) to map the filtered reads to the newly
assembled reference genome. We obtained the transcriptome assembly with
Trinity 2.8.6 (Grabherr et al., 2011) using the genome-guided bam mode
(–genome_guided_max_intron 82945). Transcripts were clustered with
CD-HIT (Fu, Niu, Zhu, Wu, & Li, 2012; W. Li & Godzik, 2006) 4.8.1 (-c
0.98) and coding regions (CDS) were predicted with TransDecoder 5.5.0
(https://github.com/TransDecoder/).