Comparative transcriptome analysis provides insight into differentially expressed genes related to cytoplasmic male sterility in broccoli (Brassica oleracea var. italica)

•A comparative transcriptome analysis of flower buds was performed using high-throughput RNA sequencing (RNA-Seq) technology in broccoli.•The differentially expressed genes and critical metabolism pathways associated with CMS were identified between the CMS line ‘WN12-95A’ (MS) and its maintainer line ‘WN12-95B’ (FS).•The results revealed that male sterility in broccoli might contribute to the presence of candidate differentially expressed genes.