Genome-wide identification and analysis of the HD-Zip transcription factor family in oats.

IF 3.9 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Frontiers in Molecular Biosciences Pub Date : 2024-10-30 eCollection Date: 2024-01-01 DOI:10.3389/fmolb.2024.1475276
Yiqun Xu, Changlai Liu
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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.

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燕麦中 HD-Zip 转录因子家族的全基因组鉴定和分析。
简介:HD-Zip转录因子是一类重要的植物转录因子,参与调控植物的生长和发育以及各种胁迫反应。为了探索燕麦 HD-Zip 转录因子的特征及其在非生物胁迫下的转录组表达模式,本研究通过生物信息学方法鉴定了燕麦基因组中的 HD-Zip 基因家族成员,并分析了它们的基本理化性质、进化关系、保守结构域、基因复制关系和表达谱:结果:在燕麦基因组中发现了74个HD-Zip基因序列,它们不均匀地分布在除4D染色体以外的所有染色体上。74 个 HD-Zip 基因可分为四个亚家族(HD-Zip Ⅰ-Ⅳ),分别包含 30 个(HD-Zip Ⅰ)、38 个(HD-Zip Ⅱ)、4 个(HD-Zip Ⅲ)和 2 个(HD-Zip Ⅳ)基因。本研究的分组结果与燕麦 HD-Zip 基因系统发生树中家族成员的聚类结果完全一致,进一步证明了序列分组的可靠性。此外,各亚科之间的保守基序和基因长度存在显著差异,但在同一亚科内则保持一致。在干旱和盐胁迫下,大量燕麦 HD-Zip 基因的表达水平被显著诱导或抑制,表明这些 HD-Zip 基因很可能参与调控燕麦对逆境的反应:本研究结果为燕麦抗性研究提供了很好的 HD-Zip 候选基因,为燕麦基因改良和遗传育种提供了参考。
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来源期刊
Frontiers in Molecular Biosciences
Frontiers in Molecular Biosciences Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
7.20
自引率
4.00%
发文量
1361
审稿时长
14 weeks
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.
期刊最新文献
Autophagy-lysosomal pathway impairment and cathepsin dysregulation in Alzheimer's disease. A matrix-centered view of mass spectrometry platform innovation for volatilome research. Genome-wide identification and analysis of the HD-Zip transcription factor family in oats. Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees. Corrigendum: Cellular heterogeneity and plasticity during NAFLD progression.
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