芝麻基因组网络资源(SesameGWR):芝麻(Sesamum indicum L.)非生物和生物胁迫反应转录组特征的完善注释数据资源。

IF 2.5 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Briefings in Functional Genomics Pub Date : 2024-12-06 DOI:10.1093/bfgp/elae022
Himanshu Avashthi, Ulavappa Basavanneppa Angadi, Divya Chauhan, Anuj Kumar, Dwijesh Chandra Mishra, Parimalan Rangan, Rashmi Yadav, Dinesh Kumar
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引用次数: 0

摘要

芝麻(Sesamum indicum L.)是一种全球栽培的油籽作物,因其历史意义和在热带和亚热带地区的广泛生长而闻名于世。芝麻具有显著的营养和药用价值,在防治营养不良、癌症、糖尿病和其他疾病(如心血管问题)方面具有良好的效果。然而,芝麻生产面临着炭腐病、干旱、盐碱和涝害等环境威胁的巨大挑战,给农民造成了经济损失。抗逆基因和途径方面的信息匮乏加剧了这些挑战。尽管芝麻非常重要,但目前还没有一个平台可以提供有关芝麻的全面信息,这极大地阻碍了对各种胁迫相关基因的挖掘和芝麻的分子育种。为了填补这一空白,我们开发了一个免费的、可通过网络访问的、用户友好型基因组网络资源(SesameGWR, http://backlin.cabgrid.res.in/sesameGWR/)。该平台提供了与生物和非生物胁迫相关的差异表达基因、转录因子、miRNA以及简单序列重复、单核苷酸多态性、插入和缺失等分子标记的关键信息。该网络资源中嵌入的功能基因组学信息和注释是通过 RNA-seq 数据分析预测的。考虑到气候变化的影响以及芝麻在营养和药用方面的重要性,这项研究对于了解胁迫响应具有极其重要的意义。SesameGWR 将成为开发气候适应性芝麻品种的宝贵工具,从而提高这种古老油籽作物的产量。
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Sesame Genomic Web Resource (SesameGWR): a well-annotated data resource for transcriptomic signatures of abiotic and biotic stress responses in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is a globally cultivated oilseed crop renowned for its historical significance and widespread growth in tropical and subtropical regions. With notable nutritional and medicinal attributes, sesame has shown promising effects in combating malnutrition cancer, diabetes, and other diseases like cardiovascular problems. However, sesame production faces significant challenges from environmental threats such as charcoal rot, drought, salinity, and waterlogging stress, resulting in economic losses for farmers. The scarcity of information on stress-resistance genes and pathways exacerbates these challenges. Despite its immense importance, there is currently no platform available to provide comprehensive information on sesame, which significantly hinders the mining of various stress-associated genes and the molecular breeding of sesame. To address this gap, here a free, web-accessible, and user-friendly genomic web resource (SesameGWR, http://backlin.cabgrid.res.in/sesameGWR/) has been developed This platform provides key insights into differentially expressed genes, transcription factors, miRNAs, and molecular markers like simple sequence repeats, single nucleotide polymorphisms, and insertions and deletions associated with both biotic and abiotic stresses.. The functional genomics information and annotations embedded in this web resource were predicted through RNA-seq data analysis. Considering the impact of climate change and the nutritional and medicinal importance of sesame, this study is of utmost importance in understanding stress responses. SesameGWR will serve as a valuable tool for developing climate-resilient sesame varieties, thereby enhancing the productivity of this ancient oilseed crop.

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来源期刊
Briefings in Functional Genomics
Briefings in Functional Genomics BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
6.30
自引率
2.50%
发文量
37
审稿时长
6-12 weeks
期刊介绍: Briefings in Functional Genomics publishes high quality peer reviewed articles that focus on the use, development or exploitation of genomic approaches, and their application to all areas of biological research. As well as exploring thematic areas where these techniques and protocols are being used, articles review the impact that these approaches have had, or are likely to have, on their field. Subjects covered by the Journal include but are not restricted to: the identification and functional characterisation of coding and non-coding features in genomes, microarray technologies, gene expression profiling, next generation sequencing, pharmacogenomics, phenomics, SNP technologies, transgenic systems, mutation screens and genotyping. Articles range in scope and depth from the introductory level to specific details of protocols and analyses, encompassing bacterial, fungal, plant, animal and human data. The editorial board welcome the submission of review articles for publication. Essential criteria for the publication of papers is that they do not contain primary data, and that they are high quality, clearly written review articles which provide a balanced, highly informative and up to date perspective to researchers in the field of functional genomics.
期刊最新文献
Sesame Genomic Web Resource (SesameGWR): a well-annotated data resource for transcriptomic signatures of abiotic and biotic stress responses in sesame (Sesamum indicum L.). A comprehensive survey of dimensionality reduction and clustering methods for single-cell and spatial transcriptomics data. AMLdb: a comprehensive multi-omics platform to identify biomarkers and drug targets for acute myeloid leukemia. Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer. Long-read RNA sequencing can probe organelle genome pervasive transcription.
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