Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Kiwifruit ( Actinidia spp.) plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rap...

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Bibliographic Details
Published in:Horticulture research 2020-08, Vol.7 (1), Article 117
Main Authors: Yue, Junyang, Liu, Jiacheng, Tang, Wei, Wu, Ya Qing, Tang, Xiaofeng, Li, Wei, Yang, Ying, Wang, Lihuan, Huang, Shengxiong, Fang, Congbing, Zhao, Kun, Fei, Zhangjun, Liu, Yongsheng, Zheng, Yi
Format: Article
Language:English
Subjects:
631/1647/2217/2018
631/1647/48
631/449/711
Actinidia
Agriculture
Annotations
Ascorbic acid
Biomedical and Life Sciences
Datasets
Ecology
Gene expression
Gene sequencing
Genomes
Genomic analysis
Homology
Interfaces
Kiwifruit
Life Sciences
Nucleotide sequence
Nutrients
Nutrition
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Plant Sciences
Ribonucleic acid
RNA
Synteny
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Summary:Kiwifruit ( Actinidia spp.) plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database (KGD; http://kiwifruitgenome.org/ ). The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies. A set of user-friendly query interfaces, analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit, which include JBrowse, a popular genome browser, and the NCBI BLAST sequence search tool. Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology (GO) term and pathway enrichment analysis.
ISSN:2662-6810
2052-7276
DOI:10.1038/s41438-020-0338-9