{"title":"大麦(Hordeum vulgare L.)Lectin Receptor-Like Kinase 基因家族的全基因组综合鉴定和硅学特征描述。","authors":"Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md Abdur Rauf Sarkar","doi":"10.1155/2024/2924953","DOIUrl":null,"url":null,"abstract":"<p><p>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 <i>LecRLK</i> genes and their regulatory elements have not been explored in a major cereal crop, barley (<i>Hordeum vulgare</i> 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 <i>LecRLK</i> genes were identified in the barley genome (referred to as <i>HvlecRLK</i>) corresponding to the <i>LecRLK</i> genes of <i>Arabidopsis thaliana</i>. These putative <i>HvlecRLK</i> genes were classified into three groups: 62 G-type <i>LecRLKs</i>, 1 C-type <i>LecRLK</i>, and 50 L-type <i>LecRLKs</i>. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type <i>HvlecRLK</i> (96.8%), C-type <i>HvlecRLK</i> (100%), and L-type <i>HvlecRLK</i> (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of <i>AtlecRLK</i>. Notably, most of the <i>HvlecRLKs</i> (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that <i>HvlecRLK</i> 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 <i>HvlecRLK</i> 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 <i>HvlecRLK</i> gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type <i>HvleckRLK64</i> and <i>HvleckRLK86</i>. 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 <i>HvleckRLK11</i> (25 for LR), <i>HvleckRLK69</i> (17 for TS), and <i>HvleckRLK80</i> (12 for HR). Additionally, <i>HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110</i> were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 <i>HvlecRLK</i> genes and <i>HvlecRLK13</i> was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 <i>Arabidopsis</i> 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.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":null,"pages":null},"PeriodicalIF":1.4000,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10914435/pdf/","citationCount":"0","resultStr":"{\"title\":\"Genome-Wide Comprehensive Identification and <i>In Silico</i> Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (<i>Hordeum vulgare</i> L.).\",\"authors\":\"Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md Abdur Rauf Sarkar\",\"doi\":\"10.1155/2024/2924953\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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 <i>LecRLK</i> genes and their regulatory elements have not been explored in a major cereal crop, barley (<i>Hordeum vulgare</i> 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 <i>LecRLK</i> genes were identified in the barley genome (referred to as <i>HvlecRLK</i>) corresponding to the <i>LecRLK</i> genes of <i>Arabidopsis thaliana</i>. These putative <i>HvlecRLK</i> genes were classified into three groups: 62 G-type <i>LecRLKs</i>, 1 C-type <i>LecRLK</i>, and 50 L-type <i>LecRLKs</i>. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type <i>HvlecRLK</i> (96.8%), C-type <i>HvlecRLK</i> (100%), and L-type <i>HvlecRLK</i> (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of <i>AtlecRLK</i>. Notably, most of the <i>HvlecRLKs</i> (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that <i>HvlecRLK</i> 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 <i>HvlecRLK</i> 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 <i>HvlecRLK</i> gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type <i>HvleckRLK64</i> and <i>HvleckRLK86</i>. 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 <i>HvleckRLK11</i> (25 for LR), <i>HvleckRLK69</i> (17 for TS), and <i>HvleckRLK80</i> (12 for HR). Additionally, <i>HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110</i> were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 <i>HvlecRLK</i> genes and <i>HvlecRLK13</i> was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 <i>Arabidopsis</i> 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.</p>\",\"PeriodicalId\":12778,\"journal\":{\"name\":\"Genetics research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.4000,\"publicationDate\":\"2024-02-27\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10914435/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genetics research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1155/2024/2924953\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q4\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genetics research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1155/2024/2924953","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
摘要
直链蛋白受体样激酶(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、信号转导和抗逆性方面发挥着至关重要的作用。然而,在主要谷类作物大麦(Hordeum vulgare L.)中,LecRLK 基因及其调控元件的全基因组鉴定和特征描述尚未得到探索。因此,本研究利用综合生物信息学工具对大麦中的 LecRLK 基因家族进行了鉴定和表征。根据系统发生树和结构域组织,在大麦基因组中总共鉴定出 113 个 LecRLK 基因(称为 HvlecRLK),与拟南芥的 LecRLK 基因相对应。这些推定的 HvlecRLK 基因被分为三组:62 个 G 型 LecRLK、1 个 C 型 LecRLK 和 50 个 L 型 LecRLK。它们不均匀地分布在八条染色体上,包括一条未知染色体,主要位于质膜(G 型 HvlecRLK(96.8%)、C 型 HvlecRLK(100%)和 L 型 HvlecRLK(98%))。对主题词组成和外显子内含子配置的分析表明,HvlecRLK 与 AtlecRLK 成员具有显著的同质性。值得注意的是,大多数 HvlecRLK(27 个 G 型,43 个 L 型)没有内含子,这表明它们具有快速功能。Ka/Ks和同源分析表明,HvlecRLK基因对是通过纯化选择进化而来的,基因复制是HvlecRLK基因家族扩大的主要因素。基因本体(GO)富集探索表明,已发现的 HvlecRLK 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。调控网络分析发现了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TFFs参与了HvlecRLK基因功能的调控。最值得注意的是,有 8 个 TFFs 被发现与 L 型 HvleckRLK64 和 HvleckRLK86 的启动子区域相连。大麦启动子顺式作用调控元件(CARE)分析共发现了 75 个 CARE 基元,分别与光响应性(LR)、组织特异性(TS)、激素响应性(HR)和胁迫响应性(SR)有关。在 HvleckRLK11(25 个对 LR 响应)、HvleckRLK69(17 个对 TS 响应)和 HvleckRLK80(12 个对 HR 响应)中发现的 CARE 数量最多。此外,预测 HvleckRLK14、HvleckRLK16、HvleckRLK33、HvleckRLK50、HvleckRLK52、HvleckRLK56 和 HvleckRLK110 在胁迫条件下会表现出更高的反应。此外,46 种推测的 miRNA 被预测为靶向 81 个 HvlecRLK 基因,其中 HvlecRLK13 是被 8 种不同的 miRNA 靶向最多的基因。蛋白质相互作用分析表明,63个HvlecRLK与拟南芥的7个STRING蛋白在功能上有较高的相似性。我们的总体研究结果为 LecRLK 基因家族提供了有价值的信息,可能为候选基因功能机制的深入研究以及育种计划中新大麦品种的开发铺平道路。
Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.).
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 LecRLK genes and their regulatory elements have not been explored in a major cereal crop, barley (Hordeum vulgare 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 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. These putative HvlecRLK genes were classified into three groups: 62 G-type LecRLKs, 1 C-type LecRLK, and 50 L-type LecRLKs. They were unevenly distributed across eight chromosomes, including one unknown chromosome, and were predominantly located in the plasma membrane (G-type HvlecRLK (96.8%), C-type HvlecRLK (100%), and L-type HvlecRLK (98%)). An analysis of motif composition and exon-intron configuration revealed remarkable homogeneity with the members of AtlecRLK. Notably, most of the HvlecRLKs (27 G-type, 43 L-type) have no intron, suggesting their rapid functionality. The Ka/Ks and syntenic analysis demonstrated that HvlecRLK 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 HvlecRLK 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 HvlecRLK gene functions. Most notably, eight TFFs were found to be linked to the promoter region of both L-type HvleckRLK64 and HvleckRLK86. 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 HvleckRLK11 (25 for LR), HvleckRLK69 (17 for TS), and HvleckRLK80 (12 for HR). Additionally, HvleckRLK14, HvleckRLK16, HvleckRLK33, HvleckRLK50, HvleckRLK52, HvleckRLK56, and HvleckRLK110 were predicted to exhibit higher responses in stress conditions. In addition, 46 putative miRNAs were predicted to target 81 HvlecRLK genes and HvlecRLK13 was the most targeted gene by 8 different miRNAs. Protein-protein interaction analysis demonstrated higher functional similarities of 63 HvlecRLKs with 7 Arabidopsis 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.
期刊介绍:
Genetics Research is a key forum for original research on all aspects of human and animal genetics, reporting key findings on genomes, genes, mutations and molecular interactions, extending out to developmental, evolutionary, and population genetics as well as ethical, legal and social aspects. Our aim is to lead to a better understanding of genetic processes in health and disease. The journal focuses on the use of new technologies, such as next generation sequencing together with bioinformatics analysis, to produce increasingly detailed views of how genes function in tissues and how these genes perform, individually or collectively, in normal development and disease aetiology. The journal publishes original work, review articles, short papers, computational studies, and novel methods and techniques in research covering humans and well-established genetic organisms. Key subject areas include medical genetics, genomics, human evolutionary and population genetics, bioinformatics, genetics of complex traits, molecular and developmental genetics, Evo-Devo, quantitative and statistical genetics, behavioural genetics and environmental genetics. The breadth and quality of research make the journal an invaluable resource for medical geneticists, molecular biologists, bioinformaticians and researchers involved in genetic basis of diseases, evolutionary and developmental studies.