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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.).

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 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.

SUBMITTER: Shan X

PROVIDER: S-EPMC6895899 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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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.).

Shan Xi X Zhang Wei W Yu Fangwei F Wang Shenyun S Li Jianbin J Tang Jun J Dai Zhongliang Z

Genes 20191108 11

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 org ...[more]

PMID: 31717469

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Project description:BackgroundThe SWEET proteins are a group of sugar transporters that play a role in sugar efflux during a range of biological processes, including stress responses. However, there has been no comprehensive analysis of the SWEET family genes in Brassica oleracea (BoSWEET), and the evolutionary pattern, phylogenetic relationship, gene characteristics of BoSWEET genes and their expression patterns under biotic and abiotic stresses remain largely unexplored.ResultsA total of 30 BoSWEET genes were identified and divided into four clades in B. oleracea. Phylogenetic analysis of the BoSWEET proteins indicated that clade II formed first, followed by clade I, clade IV and clade III, successively. Clade III, the newest clade, shows signs of rapid expansion. The Ks values of the orthologous SWEET gene pairs between B. oleracea and Arabidopsis thaliana ranged from 0.30 to 0.45, which estimated that B. oleracea diverged from A. thaliana approximately 10 to 15 million years ago. Prediction of transmembrane regions showed that eight BoSWEET proteins contain one characteristic MtN3_slv domain, twenty-one contain two, and one has four. Quantitative reverse transcription-PCR (qRT-PCR) analysis revealed that five BoSWEET genes from clades III and IV exhibited reduced expression levels under chilling stress. Additionally, the expression levels of six BoSWEET genes were up-regulated in roots of a clubroot-susceptible cabbage cultivar (CS-JF1) at 7 days after inoculation with Plasmodiophora brassicae compared with uninoculated plants, indicating that these genes may play important roles in transporting sugars into sink roots associated with P. brassicae colonization in CS-JF1. Subcellular localization analysis of a subset of BoSWEET proteins indicated that they are localized in the plasma membrane.ConclusionsThis study provides important insights into the evolution of the SWEET gene family in B. oleracea and other species, and represents the first study to characterize phylogenetic relationship, gene structures and expression patterns of the BoSWEET genes. These findings provide new insights into the complex transcriptional regulation of BoSWEET genes, as well as potential candidate BoSWEET genes that promote sugar transport to enhance chilling tolerance and clubroot disease resistance in cabbage.

Dataset Information

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

Publications

Genome-Wide Analysis of Basic Helix-Loop-Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. <i>capitat</i>a L.).

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