Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China.
University of Chinese Academy of Sciences, Beijing, China.
PLoS One. 2020 Aug 17;15(8):e0236651. doi: 10.1371/journal.pone.0236651. eCollection 2020.
WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa-IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0-7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.
WRKY 转录因子调节植物中的多种生物过程，包括非生物和生物胁迫反应，并且构成高等植物中最大的转录因子家族之一。尽管在过去的十年中，在不同物种中鉴定和功能表征 WRKY 基因方面取得了重大进展，但对高粱（Sorghum bicolor（L.）moench）中的 WRKY 家族知之甚少。在这里，我们报告了对 94 个推定的 WRKY 转录因子（SbWRKYs）的全面鉴定。根据它们的保守结构域和锌指基序类型，将 SbWRKY 分为三组（I、II 和 III），其中 II 组进一步分为五个亚组（IIa-IIe）。使用模式植物拟南芥（Arabidopsis thaliana）的 WRKY 对所有 SbWRKY 基因进行了系统发育分析。基序分析表明，所有 SbWRKY 都包含一个或两个 WRKY 结构域，并且同一组内的 SbWRKY 具有相似的基序组成。SbWRKY 基因位于高粱的 10 条染色体上，检测到一些基因簇和两个串联重复。SbWRKY 基因结构分析表明，它们包含 0-7 个内含子，大多数 SbWRKY 基因由两个内含子和三个外显子组成。GO 注释根据细胞成分、分子功能和生物过程对 SbWRKY 进行了功能分类。顺式元件分析表明，所有 SbWRKY 都至少包含一个与应激反应相关的顺式元件。我们利用公开的微阵列数据集分析了 78 个 SbWRKY 基因在不同生长阶段和不同组织中的表达谱。SbWRKY 对不同非生物胁迫的诱导表明它们可能参与应激反应。qRT-PCR 分析揭示了 SbWRKY 在干旱胁迫下的不同表达模式。对拟南芥和其他物种中功能表征的 WRKY 基因的研究将为高粱中推定的同源基因的功能表征提供线索。因此，本研究为 SbWRKY 基因的功能研究及其在干旱等关键胁迫反应中的作用提供了坚实的基础。
