Key Laboratory of Biochemistry and Molecular Biology, Biological and Agricultural College, Weifang University, Weifang, Shandong, China.
BMC Genomics. 2022 Aug 1;23(1):548. doi: 10.1186/s12864-022-08782-4.
Green-fleshed radish (Raphanus sativus L.) is an economically important root vegetable of the Brassicaceae family, and chlorophyll accumulates in its root tissues. It was reported that the basic helix-loop-helix (bHLH) transcription factors play vital roles in the process of chlorophyll metabolism. Nevertheless, a comprehensive study on the bHLH gene family has not been performed in Raphanus sativus L.
In this study, a total of 213 Raphanus sativus L. bHLH (RsbHLH) genes were screened in the radish genome, which were grouped into 22 subfamilies. 204 RsbHLH genes were unevenly distributed on nine chromosomes, and nine RsbHLH genes were located on the scaffolds. Gene structure analysis showed that 25 RsbHLH genes were intron-less. Collineation analysis revealed the syntenic orthologous bHLH gene pairs between radish and Arabidopsis thaliana/Brassica rapa/Brassica oleracea. 162 RsbHLH genes were duplicated and retained from the whole genome duplication event, indicating that the whole genome duplication contributed to the expansion of the RsbHLH gene family. RNA-seq results revealed that RsbHLH genes had a variety of expression patterns at five development stages of green-fleshed radish and white-fleshed radish. In addition, the weighted gene co-expression network analysis confirmed four RsbHLH genes closely related to chlorophyll content.
A total of 213 RsbHLH genes were identified, and we systematically analyzed their gene structure, evolutionary and collineation relationships, conserved motifs, gene duplication, cis-regulatory elements and expression patterns. Finally, four bHLH genes closely involved in chlorophyll content were identified, which may be associated with the photosynthesis of the green-fleshed radish. The current study would provide valuable information for further functional exploration of RsbHLH genes, and facilitate clarifying the molecular mechanism underlying photosynthesis process in green-fleshed radish.
绿皮萝卜（Raphanus sativus L.）是十字花科经济上重要的根茎类蔬菜，叶绿素积累在其根组织中。据报道，碱性螺旋-环-螺旋（bHLH）转录因子在叶绿素代谢过程中起着至关重要的作用。然而，对 Raphanus sativus L.中的 bHLH 基因家族尚未进行全面研究。
本研究在萝卜基因组中筛选到 213 个 Raphanus sativus L. bHLH（RsbHLH）基因，分为 22 个亚家族。204 个 RsbHLH 基因不均匀分布在 9 条染色体上，9 个 RsbHLH 基因位于支架上。基因结构分析表明，25 个 RsbHLH 基因无内含子。共线性分析显示萝卜与拟南芥/甘蓝/白菜之间的同源 bHLH 基因对。162 个 RsbHLH 基因是从全基因组复制事件中复制并保留下来的，表明全基因组复制有助于 RsbHLH 基因家族的扩张。RNA-seq 结果表明，162 个 RsbHLH 基因在绿皮萝卜和白皮萝卜的五个发育阶段具有多种表达模式。此外，加权基因共表达网络分析证实了四个与叶绿素含量密切相关的 RsbHLH 基因。
共鉴定出 213 个 RsbHLH 基因，我们系统地分析了它们的基因结构、进化和共线性关系、保守基序、基因复制、顺式调控元件和表达模式。最后，鉴定出四个与叶绿素含量密切相关的 bHLH 基因，它们可能与绿皮萝卜的光合作用有关。本研究将为进一步探索 RsbHLH 基因的功能提供有价值的信息，并有助于阐明绿皮萝卜光合作用的分子机制。
