Total RNA was extracted with TRIzol (Invitrogen, California, USA) from the bacterial samples, according to the manufacturer's instructions. Genomic DNA contamination was removed by using RNase-free DNase I (Ambion, Inc., Texas, USA) following  the manufacturer's instructions. Ribosomal RNA was removed from the total RNA using the Ribozero Kit following the manufacturer's protocol. Purified mRNA from the bacterial samples was used for transcriptome sequencing, and the library was constructed by using Illumina HiSeq 4000 at the Beijing Genomics Institute. After filtering, the remaining clean reads were stored in FASTQ (Cock et al., 2010) format and Trinity was used to perform de novo assembly with clean reads. Then, gene family clustering was performed with Tgicl to get the final unigenes. Differentially expressed genes (DEGs) were detected with NOIseq, which is based on a noisy distribution model, as described in a previous study (Tarazona et al., 2011). Hierarchical clustering was carried out for DEGs using a heatmap, which is a function of R. For clustering more than two groups, the intersection and union DEGs between them were shown on the heatmap.