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Article|01 Aug 2020|OPEN
Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics
Junyang Yue1,2, Jiacheng Liu3, Wei Tang1, Ya Qing Wu3, Xiaofeng Tang2, Wei Li1, Ying Yang1, Lihuan Wang1, Shengxiong Huang2, Congbing Fang1, Kun Zhao3, Zhangjun Fei3,4,, Yongsheng Liu2,5, & Yi Zheng3,6,7,
1School of Horticulture, Anhui Agricultural University, Hefei 230036, China
2School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
3Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
4USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
5Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
6Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
7Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China

Horticulture Research 7,
Article number: 20117 (2020)
doi: 10.1038/hortres.2020.117
Views: 290

Received: 26 Feb 2020
Revised: 12 Apr 2020
Accepted: 01 May 2020
Published online: 01 Aug 2020

Abstract

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.