School of Biological Sciences and Biotechnology, Minnan Normal University, 36 Xian-Qian-Zhi Street, Zhangzhou, 363000, Fujian, China.
School of Life Sciences, Tsinghua University, Beijing, 100084, China.
BMC Plant Biol. 2018 Nov 29;18(1):309. doi: 10.1186/s12870-018-1529-5.
The basic helix-loop-helix transcription factors play important roles in diverse cellular and molecular processes. Comparative functional genomics can provide powerful approaches to draw inferences about gene function and evolution among species. The comprehensive comparison of bHLH gene family in different gramineous plants has not yet been reported.
In this study, a total of 183, 231 and 571 bHLHs were identified in rice, maize and wheat genomes respectively, and 1154 bHLH genes from the three species and Arabidopsis were classified into 36 subfamilies. Of the identified genes, 110 OsbHLHs, 188 ZmbHLHs and 209 TabHLHs with relatively high mRNA abundances were detected in one or more tissues during development, and some of them exhibited tissue-specific expression such as TabHLH454-459, ZmbHLH099-101 and OsbHLH037 in root, TabHLH559-562, - 046, - 047 and ZmbHLH010, - 072, - 226 in leaf, TabHLH216-221, - 333, - 335, - 340 and OsbHLH005, - 141 in inflorescence, TabHLH081, ZmbHLH139 and OsbHLH144 in seed. Forty five, twenty nine and thirty one differentially expressed bHLHs were respectively detected in wheat, maize and rice under drought stresses using RNA-seq technology. Among them, the expressions of TabHLH046, - 047, ZmbHLH097, - 098, OsbHLH006 and - 185 were strongly induced, whereas TabHLH303, - 562, ZmbHLH155, - 154, OsbHLH152 and - 113 showed significant down-regulation. Twenty two TabHLHs were induced after stripe rust infection at 24 h and nine of them were suppressed at 72 hpi, whereas 28 and 6 TabHLHs exhibited obviously down- and up-regulation after powdery mildew attack respectively. Forty one ZmbHLHs were differentially expressed in response to F. verticillioides infection. Twenty two co-expression modules were identified by the WGCNA, some of which were associated with particular tissue types. And GO enrichment analysis for the modules showed that some TabHLHs were involved in the control of several biological processes, such as tapetal PCD, lipid metabolism, iron absorption, stress responses and signal regulation.
The present study identifies the bHLH family in rice, maize and wheat genomes, and detailedly discusses the evolutionary relationships, expression and function of bHLHs. This study provides some novel and detail information about bHLHs, and may facilitate understanding the molecular basis of the plant growth, development and stress physiology.
碱性螺旋-环-螺旋转录因子在多种细胞和分子过程中发挥重要作用。比较功能基因组学可以为推断物种间的基因功能和进化提供有力的方法。不同禾本科植物 bHLH 基因家族的综合比较尚未报道。
本研究分别在水稻、玉米和小麦基因组中鉴定了 183、231 和 571 个 bHLH，来自三种作物和拟南芥的 1154 个 bHLH 基因被分类为 36 个亚家族。在发育过程中，110 个 OsbHLHs、188 个 ZmbHLHs 和 209 个 TabHLHs 在一种或多种组织中具有相对较高的 mRNA 丰度，其中一些基因表现出组织特异性表达，如根中的 TabHLH454-459、ZmbHLH099-101 和 OsbHLH037，叶中的 TabHLH559-562、-046、-047 和 ZmbHLH010、-072、-226，花序中的 TabHLH216-221、-333、-335、-340 和 OsbHLH005、-141，种子中的 TabHLH081、ZmbHLH139 和 OsbHLH144。利用 RNA-seq 技术分别在小麦、玉米和水稻中检测到 45、29 和 31 个差异表达的 bHLH 在干旱胁迫下。其中，TabHLH046、-047、ZmbHLH097、-098、OsbHLH006 和-185 的表达强烈诱导，而 TabHLH303、-562、ZmbHLH155、-154、OsbHLH152 和-113 则明显下调。条锈菌侵染后 24 h 有 22 个 TabHLH 被诱导，72 hpi 时有 9 个被抑制，而白粉病攻击后有 28 个和 6 个 TabHLH 分别明显下调和上调。41 个 ZmbHLH 对 F. verticillioides 感染有差异表达。通过 WGCNA 鉴定了 22 个共表达模块，其中一些与特定的组织类型相关。模块的 GO 富集分析表明，一些 TabHLH 参与了几个生物过程的调控，如绒毡层 PCD、脂质代谢、铁吸收、应激反应和信号调节。
本研究在水稻、玉米和小麦基因组中鉴定了 bHLH 家族，并详细讨论了 bHLH 的进化关系、表达和功能。本研究提供了一些关于 bHLH 的新的详细信息，可能有助于理解植物生长、发育和应激生理的分子基础。
