Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
Genet Res (Camb). 2024 Feb 27;2024:2924953. doi: 10.1155/2024/2924953. eCollection 2024.
Lectin receptor-like kinases (LecRLKs) are a significant subgroup of the receptor-like kinases (RLKs) protein family. They play crucial roles in plant growth, development, immune responses, signal transduction, and stress tolerance. However, the genome-wide identification and characterization of genes and their regulatory elements have not been explored in a major cereal crop, barley ( L.). Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 genes were identified in the barley genome (referred to as ) corresponding to the genes of . These putative genes were classified into three groups: 62 G-type , 1 C-type , and 50 L-type . They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type (96.8%), C-type (100%), and L-type (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of . Notably, most of the (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that gene pairs evolved through purifying selection and gene duplication was the major factor for the expansion of the HvlecRLK gene family. Exploration of gene ontology (GO) enrichment indicated that the identified genes are associated with various cellular processes, metabolic pathways, defense mechanisms, kinase activity, catalytic activity, ion binding, and other essential pathways. The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type and . The promoter cis-acting regulatory element (CARE) analysis of barley identified a total of 75 CARE motifs responsive to light responsiveness (LR), tissue-specific (TS), hormone responsiveness (HR), and stress responsiveness (SR). The maximum number of CAREs was identified in (25 for LR), (17 for TS), and (12 for HR). Additionally, were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 genes and was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 STRING proteins. Our overall findings provide valuable information on the LecRLK gene family which might pave the way to advanced research on the functional mechanism of the candidate genes as well as to develop new barley cultivars in breeding programs.
凝集素受体样激酶(LecRLKs)是受体样激酶(RLKs)蛋白家族的一个重要亚群。它们在植物生长、发育、免疫反应、信号转导和应激耐受中发挥着关键作用。然而,在主要的谷物作物大麦( L.)中,尚未对基因及其调控元件进行全基因组鉴定和特征描述。因此,在这项研究中,我们使用集成的生物信息学工具来鉴定和描述大麦中的 LecRLK 基因家族。基于系统发育树和结构域组织,在大麦基因组中鉴定到了 113 个基因(称为),这些基因对应于拟南芥中的 107 个基因。这些假定的 113 个基因被分为三组:62 个 G 型、1 个 C 型和 50 个 L 型。它们不均匀地分布在 8 条染色体上,包括一条未知染色体,并且主要位于质膜上(G 型 96.8%、C 型 100%和 L 型 98%)。对基序组成和外显子-内含子结构的分析表明,它们与其他的成员具有显著的同源性。值得注意的是,大多数 113 个基因(27 个 G 型、43 个 L 型)没有内含子,这表明它们具有快速的功能。Ka/Ks 分析和共线性分析表明,基因对通过纯化选择进化,基因复制是扩大 HvlecRLK 基因家族的主要因素。基因本体论(GO)富集分析表明,鉴定出的基因与各种细胞过程、代谢途径、防御机制、激酶活性、催化活性、离子结合和其他重要途径有关。调控网络分析确定了 29 个转录因子家族(TFFs),其中包括 bZIP、C2H2、ERF、MIKC_MADS、MYB、NAC 和 WRKY 在内的 7 个主要 TFF 参与了基因功能的调控。值得注意的是,发现了 8 个 TFF 与 L 型和 基因的启动子区域相关联。大麦的顺式作用调控元件(CARE)分析总共鉴定出 75 个对光响应(LR)、组织特异性(TS)、激素响应(HR)和应激响应(SR)有反应的 CARE 基序。在 (25 个用于 LR)、 (17 个用于 TS)和 (12 个用于 HR)中鉴定到最多的 CARE。此外,预测 基因在应激条件下表现出更高的响应。此外,预测 46 个候选 miRNA 靶向 81 个基因, 是 8 个不同 miRNA 最靶向的基因。蛋白质-蛋白质相互作用分析表明,63 个 HvlecRLKs 与 7 个 STRING 蛋白具有更高的功能相似性。我们的综合研究结果提供了关于 LecRLK 基因家族的有价值的信息,这可能为候选基因的功能机制研究以及在育种计划中开发新的大麦品种铺平道路。