CitGVD: a comprehensive database of citrus genomic variations

Qiang Li,Xiuping Zou,Anhua Hu,Shanchun Chen,Xiujuan Qin,Aihong Peng,Guojin Jiang,Lanzhen Xu,Jingjing Qi,Wanfu Dou,Qin Long,Lixiao Yao,Yongrui He,Ruirui Jia,Tiangang Lei

doi:10.1038/s41438-019-0234-3

Qiang Li, Xiuping Zou + Show 13 more

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https://doi.org/10.1038/s41438-019-0234-3

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Citrus is one of the most important commercial fruit crops worldwide. With the vast genomic data currently available for citrus fruit, genetic relationships, and molecular markers can be assessed for the development of molecular breeding and genomic selection strategies. In this study, to permit the ease of access to these data, a web-based database, the citrus genomic variation database (CitGVD, http://citgvd.cric.cn/home) was developed as the first citrus-specific comprehensive database dedicated to genome-wide variations including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs). The current version (V1.0.0) of CitGVD is an open-access resource centered on 1,493,258,964 high-quality genomic variations and 84 phenotypes of 346 organisms curated from in-house projects and public resources. CitGVD integrates closely related information on genomic variation annotations, related gene annotations, and details regarding the organisms, incorporating a variety of built-in tools for data accession and analysis. As an example, CitGWAS can be used for genome-wide association studies (GWASs) with SNPs and phenotypic data, while CitEVOL can be used for genetic structure analysis. These features make CitGVD a comprehensive web portal and bioinformatics platform for citrus-related studies. It also provides a model for analyzing genome-wide variations for a wide range of crop varieties.

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Citrus is grown in more than 100 countries
CitGVD provides in-depth analysis, including CitTRAIT for phenotypic data statistics, CitGWAS for genome-wide association studies (GWASs) based on built-in data, CitEVOL for genetic evolution analysis, PCR primer design and Gbrowse for variations and genes
BROWSE Under the “BROWSE” pull-down menu, CitGVD provides data browsing functionalities, including single nucleotide polymorphisms (SNPs)/INDEL browse, designed for the statistics of genomic variations according to chromosomes, types and germplasms, gene annotation browse for gene information and annotations, and germplasm browse for browsing germplasm details, including germplasm ID, name, origin, type and other information

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Citrus is grown in more than 100 countries. The worldwide production and total acreage of citrus fruits ranks first among all fruit crops. Such a platform should include abundant data on high-quality genomic variations and detailed genotype/phenotype information for an abundance of citrus accessions. CitGVD includes large sets of data on genomic variations (SNPs and INDELs) compiled from two released reference genomes for Citrus clementina and Citrus grandis[2], including 84 phenotypes, gene functional annotations and informative literature.

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