bHLH domain contains approximately 60 amino acids with two functionally distinct regions of the HLH region and the basic region (Murre et al., 1989 Ledent and Vervoort, 2001). The bHLH protein is a kind of transcription factor, and it has DNA binding and dimerization capabilities as bHLH domain existed. We also performed a cis-acting regulatory element analysis on some genes involved in flavonoid or anthocyanin biosynthesis and our results showed that most of these gene promoters contained G-box or E-box elements that could be recognized by bHLH family members. Based on the GO or Nr function annotations, we found three other genes that are potentially related to anthocyanin or flavonol biosynthesis: VvbHLH003, VvbHLH007, and VvbHLH010. Twenty-two grape bHLH genes could be induced by PEG treatment and 17 grape bHLH genes could be induced by cold stress treatment including a homologous form of MYC2, VvbHLH007. Nine triplicate gene groups were found in the grape bHLH gene family and all of these triplicate gene groups underwent purifying selection. 41 duplicate gene pairs were found in the grape bHLH gene family, and all of these duplicate gene pairs underwent purifying selection. Phylogenetic analyses placed the genes into 15 clades, with some remaining orphans. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. In grapes ( Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis.
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