Total RNA was extracted from the TW, OW and NW using an RNA reagent kit (DP441; Tiangen Biotech, Beijing, China) according to the manufacturer’s protocol. Nine transcriptome libraries were constructed for 150-bp paired-end Illumina high-throughput sequencing of mRNAs and lncRNAs using the Illumina HiSeq™ 4000 platform (Illumina, USA) by Gene Denovo Biotechnology Co. (Guangzhou, China). The post sequencing data filtering and analysis methodology have been described in a previous study [57 (link)]. Cufflinks and Cuffcompare software [58 (link), 59 (link)] were used to assemble transcripts and compare sequences to known sequences in the C. bungei genome (unpublished). The fragments per kilobase of transcript per million mapped reads (FPKM) value was used as an indicator to evaluate gene expression [59 (link)]. In the present study, transcripts with a fold change of ≥1.5 or ≤ − 1.5 and a P value of < 0.05 between various comparison groups were considered significant DEGs.
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