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

Junyang Yue,Wei Li,Jiacheng Liu,Wei Tang,Shengxiong Huang,Xiaofeng Tang,Zhangjun Fei,Yongsheng Liu,Congbing Fang,Yi Zheng,Lihuan Wang,Ya Qing Wu,Ying Yang,Kun Zhao

doi:10.1038/s41438-020-0338-9

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.

Highlights

Kiwifruit, belonging to the basal genus Actinidia within the family Actinidiaceae, consists of ~54 species and 75 taxa[1]
Comparative genomic analysis We identified syntenic blocks and homologous gene pairs within syntenic blocks in the four kiwifruit genome sequences, including comparisons both within each genome and between any two genomes
transcription factors (TFs) and transcriptional regulators (TRs) were imported into Kiwifruit Genome Database (KGD) using the gene family extension module that we developed previously

Summary

Introduction

Kiwifruit, belonging to the basal genus Actinidia within the family Actinidiaceae, consists of ~54 species and 75 taxa[1]. All species in this genus are perennial, deciduous and dioecious plants with a climbing or scrambling growth habit. They are native to southwestern China, they are prevalent in New Zealand after being introduced in the early 20th century[2]. Despite the availability of diverse, rich germplasm resources for kiwifruit, only several economically important horticultural species have been successfully domesticated and widely cultivated, including A. chinensis Planchon, A. deliciosa Kiwifruit provides a distinct model system for studies of several fundamental biological processes, such as ascorbic acid biosynthesis[5] and sex determination[6,7]

Findings

Discussion

Conclusion