{"title":"Genome-wide identification and analysis of the HD-Zip transcription factor family in oats.","authors":"Yiqun Xu, Changlai Liu","doi":"10.3389/fmolb.2024.1475276","DOIUrl":null,"url":null,"abstract":"<p><strong>Introduction: </strong>HD-Zip transcription factors are an important class of plant transcription factors involved in regulating plant growth and development as well as various stress responses. In order to explore the characteristics of oat HD-Zip transcription factors and their transcriptomic expression patterns under abiotic stress, this study identified members of the HD-Zip gene family in the oat genome through bioinformatics methods and analyzed their basic physicochemical properties, evolutionary relationships, conserved structural domains, gene duplication relationships, and expression profiles.</p><p><strong>Results: </strong>74 HD-Zip gene sequences were identified in the oat genome, unevenly distributed in all chromosomes except the 4D chromosome. The 74 HD-Zip genes can be divided into four subfamilies (HD-Zip Ⅰ-Ⅳ), containing 30 (HD-Zip Ⅰ), 38 (HD-Zip Ⅱ), 4 (HD-Zip III), and 2 (HD-Zip IV) genes, respectively. The grouping of this study is completely consistent with the clustering results of family members in the oat HD-Zip gene phylogenetic tree, further supporting the reliability of the sequence grouping. In addition, there are significant differences in conserved motifs and gene lengths between subfamilies, but they are conserved within the same subfamily. Under drought and salt stress, the expression levels of a large number of oat HD-Zip genes were significantly induced or suppressed, indicating that these HD-Zip genes are likely to be involved in regulating the oat's response to adversity.</p><p><strong>Conclusions: </strong>The results of this study provide excellent candidate HD-Zip genes for the study of oat resistance, and provide a reference for oat gene improvement and genetic breeding.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"11 ","pages":"1475276"},"PeriodicalIF":3.9000,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11557432/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Frontiers in Molecular Biosciences","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.3389/fmolb.2024.1475276","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Introduction: HD-Zip transcription factors are an important class of plant transcription factors involved in regulating plant growth and development as well as various stress responses. In order to explore the characteristics of oat HD-Zip transcription factors and their transcriptomic expression patterns under abiotic stress, this study identified members of the HD-Zip gene family in the oat genome through bioinformatics methods and analyzed their basic physicochemical properties, evolutionary relationships, conserved structural domains, gene duplication relationships, and expression profiles.
Results: 74 HD-Zip gene sequences were identified in the oat genome, unevenly distributed in all chromosomes except the 4D chromosome. The 74 HD-Zip genes can be divided into four subfamilies (HD-Zip Ⅰ-Ⅳ), containing 30 (HD-Zip Ⅰ), 38 (HD-Zip Ⅱ), 4 (HD-Zip III), and 2 (HD-Zip IV) genes, respectively. The grouping of this study is completely consistent with the clustering results of family members in the oat HD-Zip gene phylogenetic tree, further supporting the reliability of the sequence grouping. In addition, there are significant differences in conserved motifs and gene lengths between subfamilies, but they are conserved within the same subfamily. Under drought and salt stress, the expression levels of a large number of oat HD-Zip genes were significantly induced or suppressed, indicating that these HD-Zip genes are likely to be involved in regulating the oat's response to adversity.
Conclusions: The results of this study provide excellent candidate HD-Zip genes for the study of oat resistance, and provide a reference for oat gene improvement and genetic breeding.
期刊介绍：
Much of contemporary investigation in the life sciences is devoted to the molecular-scale understanding of the relationships between genes and the environment — in particular, dynamic alterations in the levels, modifications, and interactions of cellular effectors, including proteins. Frontiers in Molecular Biosciences offers an international publication platform for basic as well as applied research; we encourage contributions spanning both established and emerging areas of biology. To this end, the journal draws from empirical disciplines such as structural biology, enzymology, biochemistry, and biophysics, capitalizing as well on the technological advancements that have enabled metabolomics and proteomics measurements in massively parallel throughput, and the development of robust and innovative computational biology strategies. We also recognize influences from medicine and technology, welcoming studies in molecular genetics, molecular diagnostics and therapeutics, and nanotechnology.
Our ultimate objective is the comprehensive illustration of the molecular mechanisms regulating proteins, nucleic acids, carbohydrates, lipids, and small metabolites in organisms across all branches of life.
In addition to interesting new findings, techniques, and applications, Frontiers in Molecular Biosciences will consider new testable hypotheses to inspire different perspectives and stimulate scientific dialogue. The integration of in silico, in vitro, and in vivo approaches will benefit endeavors across all domains of the life sciences.
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