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The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as  Arabidopsis , rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts,  Arachis duranensis  (AA) and  Arachis ipaensis  (BB), respectively. Phylogenetic analysis indicated that these  bHLH s could be classified into 19 subfamilies. Distribution mapping results showed that peanut  bHLH  genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120  bHLH  gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184  bHLH  genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61  bHLH  genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development