Genome-wide identification of the bHLH transcription factor family and analysis of bHLH genes related to puerarin biosynthesis in Pueraria lobata var. thomsonii (Benth.)

Plant basic helix-loop-helix (bHLH) transcription factors are involved in diverse biological process. So far, there has been no report to systematically carry out comprehensive identification of bHLH members in Pueraria lobata var. thomsonii (Benth.) (P. thomsonii), a traditional Chinese herb that is an excellent source of puerarin. Phylogenetic analysis showed that 219 bHLH genes were identified in the P. thomsonii and classified into 13 subfamilies. All the PlbHLH genes were distributed on the 11 chromosomes unevenly and the number of PlbHLH genes on each chromosome varied from 12 to 44. Both of tandem and segmental duplications were key factors driving bHLH gene family expansion in P. thomsonii. A total of 20 conserved motifs were found in PlbHLH gene family, 185 PlbHLH members contain more than two introns, and genes within the same subfamily appeared to share similar intron-exon gene structures. The Ka/Ks analysis indicated PlbHLH gene family undergo purifying selection during evolution. Combined the RNA-seq data with the qRT-PCR detection results, PlbHLH79/148/149 were found to be the most probably candidate genes which were involved in puerarin biosynthesis pathway. Together, our study provided a good foundation for further research into the regulatory mechanism of the candidate PlbHLH proteins for puerarin biosynthesis in P. thomsonii.