The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

中文翻译：

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甘蓝型油菜 bHLH 超基因家族的全基因组调查

基本螺旋-环-螺旋 (bHLH) 基因家族是植物中最大的转录因子家族之一，在不同物种中具有功能特征。然而，人们对其在经济上重要的异源多倍体油料作物甘蓝型油菜中的功能知之甚少。我们在欧洲油菜基因组 (BnabHLHs) 中鉴定了 602 个潜在的 bHLH，并根据系统发育、蛋白质结构和外显子-内含子组织分析将它们分为 35 个亚科，其中包括 7 个新分离的亚科。分析了该基因家族的内含子插入模式，并在 BnabHLH 的 bHLH 区域中总共鉴定了八种类型。染色体分布和同线性分析表明，白菜和甘蓝之间的杂交是 BnabHLH 的主要扩增机制。表达分析表明，BnabHLH 广泛存在于不同的植物组织中，并形成七种主要模式，表明它们可能参与甘蓝型油菜发育的各个方面。此外，当根用五种不同的激素（IAA，生长素；GA3，赤霉素；6-BA，细胞分裂素；ABA，脱落酸和ACC，乙烯）处理时，BnabHLH 的表达谱发生显着变化，其中许多表现出表达增加。经过五种激素处理后，通过 qRT-PCR 证实了五种候选 BnabHLH 的诱导。通过对其表达谱和同源功能的联合分析，预测来自 9 个亚科的多达 246 个 BnabHLH 具有与根发育相关的潜在作用。从甘蓝型油菜中鉴定出的 602 个 BnabHLH 被分为 35 个亚科，来自同一亚科的成员通常具有相似的序列基序。总的来说，我们发现 BnabHLH 可能广泛参与甘蓝型油菜的根部发育。此外，这项研究为BnabHLHs超基因家族的潜在功能提供了重要的见解，因此将有助于未来的基因功能研究。