Comparative analysis of basic helix-loop-helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus
Comparative analysis of basic helix-loop-helix gene family among Brassica oleracea, Brassica rapa, and Brassica napus
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甘蓝、白菜、甘蓝型油菜基本螺旋-环-螺旋基因家族的比较分析
DOI：
10.1186/s12864-020-6572-6
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发表时间：
2020-02-24
期刊：
影响因子：
4.4
通讯作者：
Yu, Xiaolin
中科院分区：
文献类型：
--
作者：
Miao, Liming;Gao, Yingying;Yu, Xiaolin
研究背景bHLH基因是植物中第二大基因家族，部分成员在雌蕊发育及对干旱、涝渍、低温和盐胁迫的响应中发挥重要作用。bHLH基因家族已在除甘蓝和B外的许多物种中被鉴定。napus到目前为止本研究旨在确定B中的bHLH家族成员。oleracea，B. B. rapa和B. napus的遗传多样性，阐明了它们的表达、复制、生殖和进化特征。结果在B.甘蓝，B有440个基因。在B中有251个基因。rapa，包括21个新的bHLH成员，已被确定。系统发育树分析、保守基序分析和基因结构分析表明，同一亚科内的成员高度保守。同源基因的Ka/Ks值大多< 1，表明这些基因受到了较强的保留纯化选择。BrabHLH和BolbHLH基因的保留率分别为51.6%和55.1%。B. rapa和B.在根中的表达模式相似，而在茎、叶和生殖组织中的表达模式则相反。另外，在阿坝和JA处理下分别有41个和30个bHLH基因差异表达，下调基因数量显著多于上调基因。结论本研究对B人群中的bHLH基因家族进行了鉴定和比较基因组学分析。oleracea，B. B. rapa和B. napus，并调查了它们的多样性。B. rapa和B.在根中的表达模式相似，而在茎、叶和生殖组织中的表达模式相反。进一步的分析表明，bHLH基因的一些成员可能在非生物和生物胁迫条件下发挥关键作用。这是首次报道在B中进行bHLH基因家族分析。oleracea和B.为bHLH基因在植物中的功能研究提供了有用的信息。
Background The basic helix-loop-helix (bHLH) is the second largest gene family in the plant, some members play important roles in pistil development and response to drought, waterlogging, cold stress and salt stress. The bHLH gene family has been identified in many species, except for Brassica oleracea and B. napus thus far. This study aims to identify the bHLH family members in B. oleracea, B. rapa and B. napus, and elucidate the expression, duplication, phylogeny and evolution characters of them. Result A total of 268 bHLH genes in B. oleracea, 440 genes in B. napus, and 251 genes in B. rapa, including 21 new bHLH members, have been identified. Subsequently, the analyses of the phylogenetic trees, conserved motifs and gene structures showed that the members in the same subfamily were highly conserved. Most Ka/Ks values of homologous gene were < 1, which indicated that these genes suffered from strong purifying selection for retention. The retention rates of BrabHLH and BolbHLH genes were 51.6 and 55.1%, respectively. The comparative expression patterns between B. rapa and B. napus showed that they had similar expression patterns in the root and contrasting patterns in the stems, leaves, and reproductive tissues. In addition, there were 41 and 30 differential expression bHLH genes under the treatments of ABA and JA, respectively, and the number of down regulation genes was significantly more than up regulation genes. Conclusion In the present study, we identified and performed the comparative genomics analysis of bHLH gene family among B. oleracea, B. rapa and B. napus, and also investigated their diversity. The expression patterns between B. rapa and B. napus shows that they have the similar expression pattern in the root and opposite patterns in the stems, leaves, and reproduction tissues. Further analysis demonstrated that some bHLH gene members may play crucial roles under the abiotic and biotic stress conditions. This is the first to report on the bHLH gene family analysis in B. oleracea and B. napus, which can offer useful information on the functional analysis of the bHLH gene in plants.