Comparison across four possible reference transcriptomes generated from the de novo assembly for gene expression studies.

Reference transcriptomes—“Full”: complete de novo Trinity assembly; “Pred. genes”: retained a single (longest) isoform each Trinity-defined unique genes; “Full-CDS”: de novo Trinity assembly filtered using TransDecoder with only transcripts with predicted coding regions retained; “Pred. genes-CDS”: “Pred. genes” transcriptome filtered using TransDecoder with only transcripts with predicted coding regions retained. Number of transcripts, Bowtie mapping statistics and BUSCO analysis is given for each reference. Differential gene expression results include the number of transcripts that were included in the statistical analysis (expression level: > 1 cpm) and number of identified differentially expressed genes (DEGS) using either Bowtie or kallisto software as the mapping program.