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SapBase: A central portal for functional and comparative genomics of Sapindaceae species.

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Title: SapBase: A central portal for functional and comparative genomics of Sapindaceae species.
Authors: Li, Jiawei, Chen, Chengjie, Zeng, Zaohai, Wu, Fengqi, Feng, Junting, Liu, Bo, Mai, Yingxiao, Chu, Xinyi, Wei, Wanchun, Li, Xin, Liang, Yanyang, Liu, YuanLong, Xu, Jing, Xia, Rui
Source: Journal of Integrative Plant Biology; Aug2024, Vol. 66 Issue 8, p1561-1570, 10p
Subject Terms: GENOMICS, MYB gene, FUNCTIONAL genomics, GENE expression profiling, NON-coding RNA
Abstract: 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. [ABSTRACT FROM AUTHOR]
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Database: Complementary Index
Description
Abstract: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. [ABSTRACT FROM AUTHOR]
ISSN:16729072
DOI:10.1111/jipb.13680