Total RNA was isolated using MicroRNA easy Kit (Qiagen, Germany) following the manufacturer's instructions. The ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, US). Sequencing library was constructed using VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme Biotech, China). The library was then sequenced on an Illumina HiSeq4000 platform, generating 100 bp paired-end reads.
Bowtie2 v2.3.5 (43 (link)) was used to map the raw reads against the reference genomes (see accession number above). The normalized expression abundance of each gene was estimated by RSEM v1.3.1 (44 ). The Integrative Genomics Viewer v2.3 (45 ) was used to view the alignment and check if the transcribed sequences were identical to genome sequence and if any mutation events occurred at the transcription stage. The transcription start sites were predicted using Rockhopper software (46 (link)); the transcriptome data for all strains used the genome of 14028S (accession no. NC_016856) as the reference. The prediction results were listed in theSupplementary Table S1 .
Bowtie2 v2.3.5 (43 (link)) was used to map the raw reads against the reference genomes (see accession number above). The normalized expression abundance of each gene was estimated by RSEM v1.3.1 (44 ). The Integrative Genomics Viewer v2.3 (45 ) was used to view the alignment and check if the transcribed sequences were identical to genome sequence and if any mutation events occurred at the transcription stage. The transcription start sites were predicted using Rockhopper software (46 (link)); the transcriptome data for all strains used the genome of 14028S (accession no. NC_016856) as the reference. The prediction results were listed in the
