Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh.
PLoS One. 2024 Aug 26;19(8):e0309353. doi: 10.1371/journal.pone.0309353. eCollection 2024.
Formin proteins, characterized by the FH2 domain, are critical in regulating actin-driven cellular processes and cytoskeletal dynamics during abiotic stress. However, no genome-wide analysis of the formin gene family has yet to be conducted in the economically significant plant potato (Solanum tuberosum L.). In this study, 26 formin genes were identified and characterized in the potato genome (named as StFH), each containing the typical FH2 domain and distributed across the ten chromosomes. The StFH was categorized into seven subgroups (A-G) and the gene structure and motif analysis demonstrated higher structural similarities within the subgroups. Besides, the StFH exhibited ancestry and functional similarities with Arabidopsis. The Ka/Ks ratio indicated that StFH gene pairs were evolving through purifying selection, with five gene pairs exhibiting segmental duplications and two pairs exhibiting tandem duplications. Subcellular localization analysis suggested that most of the StFH genes were located in the chloroplast and plasma membrane. Moreover, 54 cis-acting regulatory elements (CAREs) were identified in the promoter regions, some of which were associated with stress responses. According to gene ontology analysis, the majority of the StFH genes were involved in biological processes, with 63 out of 74 GO terms affecting actin polymerization. Six major transcription factor families, including bZIP, C2H2, ERF, GATA, LBD, NAC, and HSF, were identified that were involved in the regulation of StFH genes in various abiotic stresses, including drought. Further, the 60 unique microRNAs targeted 24 StFH by regulating gene expression in response to drought stress were identified. The expression of StFH genes in 14 different tissues, particularly in drought-responsive tissues such as root, stem, shoot apex, and leaf, underscores their significance in managing drought stress. RNA-seq analysis of the drought-resistant Qingshu No. 9 variety revealed the potential role of up-regulated genes, including StFH2, StFH10, StFH19, and StFH25, in alleviating drought stress. Overall, these findings provide crucial insights into the response to drought stress in potatoes and can be utilized in breeding programs to develop potato cultivars with enhanced drought-tolerant traits.
formin 蛋白，其特征在于 FH2 结构域，在调控非生物胁迫下细胞过程和细胞骨架动力学中起着关键作用。然而，在经济上重要的植物马铃薯（Solanum tuberosum L.）中，尚未对formin 基因家族进行全基因组分析。在这项研究中，在马铃薯基因组中鉴定和表征了 26 个formin 基因（命名为 StFH），每个基因都包含典型的 FH2 结构域，并分布在十个染色体上。StFH 被分为七个亚组（A-G），基因结构和基序分析表明亚组内具有更高的结构相似性。此外，StFH 与拟南芥具有亲缘关系和功能相似性。Ka/Ks 比值表明 StFH 基因对通过纯化选择进化，有 5 对基因对表现出片段重复，有 2 对基因对表现出串联重复。亚细胞定位分析表明，大多数 StFH 基因位于叶绿体和质膜中。此外，在启动子区域鉴定了 54 个顺式作用调控元件（CAREs），其中一些与应激反应有关。根据基因本体论分析，大多数 StFH 基因参与了生物过程，其中 74 个 GO 术语中的 63 个影响肌动蛋白聚合。鉴定出 6 个主要的转录因子家族，包括 bZIP、C2H2、ERF、GATA、LBD、NAC 和 HSF，它们参与了各种非生物胁迫下 StFH 基因的调节，包括干旱胁迫。进一步，鉴定了 60 个独特的 microRNAs 通过调节基因表达来靶向 24 个 StFH 基因，以响应干旱胁迫。在 14 种不同组织中的 StFH 基因表达，特别是在干旱响应组织如根、茎、芽和叶中，强调了它们在管理干旱胁迫方面的重要性。对耐旱品种 Qingshu No.9 的 RNA-seq 分析揭示了上调基因（包括 StFH2、StFH10、StFH19 和 StFH25）在缓解干旱胁迫中的潜在作用。总的来说，这些发现为马铃薯对干旱胁迫的反应提供了重要的见解，并可用于培育计划，以开发具有增强耐旱特性的马铃薯品种。
