Abstract
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 24 h 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.
Highlights
Brassica oleracea is widely grown all over the world, including cabbage (B. oleracea var. capitata), kale (B. oleracea var. acephala), Brussels sprout (B. oleracea var. gemmifera), cauliflower (B. oleracea var.botrytis), and broccoli (B. oleracea var. italica)
For the genome-wide identification of BobHLH genes, 234 available protein sequences were identified from the B. oleracea genome
We investigated the cis-acting elements in chilling-responsive BobHLH genes (Figure 7), ABRE element plays an important role in ABA signaling and response to drought in A. thaliana [61], almost all of the BobHLH genes contained ABA-responsive element
Summary
Brassica oleracea is widely grown all over the world, including cabbage (B. oleracea var. capitata), kale (B. oleracea var. acephala), Brussels sprout (B. oleracea var. gemmifera), cauliflower (B. oleracea var.botrytis), and broccoli (B. oleracea var. italica). B. oleracea is one of the most important leafy vegetable crops for studying morphological diversity and polyploidy evolution because of its unique U’s triangle theory and the Brassica lineage-specific whole-genome triplication (WGT) event [1]. Genes 2019, 10, 914 plant growth and stress responses are coordinated by the combination of different network regulators, such as transcription factors (TFs). TFs can recognize and bind the gene promoters in the nucleus, regulating the temporal and spatial expression of genes [3,4,5]. TFs respond to plant physiological, biochemical, and stress conditions by activating or inhibiting the associated downstream genes [5,6,7]. The basic helix–loop–helix (bHLH) TF is one of the largest families of TFs in plants [4]
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