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Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

1
Zhenjiang Agricultural Research Institute, Jurong 212400, China
2
Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(11), 914; https://doi.org/10.3390/genes10110914
Received: 26 October 2019 / Accepted: 5 November 2019 / Published: 8 November 2019
(This article belongs to the Section Plant Genetics and Genomics)
Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.
Keywords: cabbage (Brassica oleracea var. capitata L.); bHLH transcription factor; chilling stress; RNA-Seq cabbage (Brassica oleracea var. capitata L.); bHLH transcription factor; chilling stress; RNA-Seq
MDPI and ACS Style

Shan, X.; Zhang, W.; Yu, F.; Wang, S.; Li, J.; Tang, J.; Dai, Z. Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.). Genes 2019, 10, 914.

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