SapBase:无患子科物种功能和比较基因组学的中心门户。

IF 9.3 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Integrative Plant Biology Pub Date : 2024-05-28 DOI:10.1111/jipb.13680
Jiawei Li, Chengjie Chen, Zaohai Zeng, Fengqi Wu, Junting Feng, Bo Liu, Yingxiao Mai, Xinyi Chu, Wanchun Wei, Xin Li, Yanyang Liang, YuanLong Liu, Jing Xu, Rui Xia
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引用次数: 0

摘要

无患子科包括草本、藤本、灌木和乔木等多种植物形态,广泛分布于热带和亚热带地区。该科植物包括荔枝、龙眼、红毛丹和橡子等具有重要经济价值的作物。近年来,随着基因组学技术的广泛应用,一些无患子科植物的基因组已被解码,从而在该领域积累了大量的组学数据。数据的激增凸显了对能够存储、共享和分析这些数据的统一基因组数据中心的迫切需要。在此,我们介绍 SapBase,即无患子科基因组数据库。SapBase 收录了七个已发表的植物基因组及其相应的基因结构和功能注释、小 RNA 注释、基因表达谱、基因通路和同源区块信息。它为基因信息挖掘、共表达分析和种间比较基因组分析提供了用户友好的功能。此外,我们还通过对荔枝中的一个 MYB 基因进行详细的生物信息学分析,展示了 SapBase 的广泛功能。因此,SapBase 可以作为一个综合基因组资源和分析平台,用于无患子科物种的科学探索及其与其他植物的比较研究。
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SapBase: A central portal for functional and comparative genomics of Sapindaceae species

The Sapindaceae family, encompassing a wide range of plant forms such as herbs, vines, shrubs, and trees, is widely distributed across tropical and subtropical regions. This family includes economically important crops like litchi, longan, rambutan, and ackee. With the wide application of genomic technologies in recent years, several Sapindaceae plant genomes have been decoded, leading to an accumulation of substantial omics data in this field. This surge in data highlights the pressing need for a unified genomic data center capable of storing, sharing, and analyzing these data. Here, we introduced SapBase, that is, the Sapindaceae Genome Database. SapBase houses seven published plant genomes alongside their corresponding gene structure and functional annotations, small RNA annotations, gene expression profiles, gene pathways, and synteny block information. It offers user-friendly features for gene information mining, co-expression analysis, and inter-species comparative genomic analysis. Furthermore, we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in litchi. Thus, SapBase could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.

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来源期刊
Journal of Integrative Plant Biology
Journal of Integrative Plant Biology 生物-生化与分子生物学
CiteScore
18.00
自引率
5.30%
发文量
220
审稿时长
3 months
期刊介绍: Journal of Integrative Plant Biology is a leading academic journal reporting on the latest discoveries in plant biology.Enjoy the latest news and developments in the field, understand new and improved methods and research tools, and explore basic biological questions through reproducible experimental design, using genetic, biochemical, cell and molecular biological methods, and statistical analyses.
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