Citrus Pan-Genome to Breeding Database (CPBD): A comprehensive genome database for citrus breeding

The genus Citrus comprises more than 30 species worldwide ( Swingle, 1943 Swingle W.T. The botany of Citrus and its wild relatives in the orange subfamily. Citrus Ind. 1943; 1: 128-474 Google Scholar ). However, citrus genetics and traditional breeding are hindered due to asexual reproduction, long generation time, and empirical utilization of the germplasm. The whole-genome information of different citrus species accelerates the genetic studies and improves the breeding efficiency by high-density markers. We had published the draft genome of the Citrus sinensis ( Xu et al., 2013 Xu Q. Chen L.-L. Ruan X. Chen D. Zhu A. Chen C. Bertrand D. Jiao W.-B. Hao B.-H. Lyon M.P. et al. The draft genome of sweet orange (Citrus sinensis). Nat. Genet. 2013; 45: 59-66 Crossref PubMed Scopus (727) Google Scholar ) and Citrus sinensis Annotation Project database ( Wang et al., 2014 Wang J. Chen D. Lei Y. Chang J.-W. Hao B.-H. Xing F. Li S. Xu Q. Deng X.-X. Chen L.-L. Citrus sinensis annotation Project (CAP): a comprehensive database for sweet orange genome. PLoS One. 2014; 9: e87723 Crossref PubMed Scopus (45) Google Scholar ) to provide a preliminary platform for such a purpose. However, there are only a few databases specially designed for citrus. The Citrus Genome Database (https://www.citrusgenomedb.org) contains 25 citrus genomes as well as plentiful markers, phenotypes of citrus species, and quantitative trait loci of agronomic traits. CitGVD (http://citgvd.cric.cn/home) mainly centers on SNPs and insertions or deletions (indels) of citrus species, while citSATdb (http://bioinfo.usu.edu/citSATdb/) mostly focuses on molecular markers mined from 6 citrus species. Data of gene expression, genomic variations, and DNA methylome of citrus as well as tools for CRISPR, KEGG/GO Enrichment, and genome-wide association studies (GWASs) are necessary for a comprehensive database. Recently, we updated genome information of Citrus sinensis (two new versions) ( Wang et al., 2021 Wang L. Huang Y. Liu Z. He J. Jiang X. He F. Lu Z. Yang S. Chen P. Yu H. et al. Somatic variations led to the selection of acidic and acidless orange cultivars. Native Plants. 2021; 7: 954-965 Crossref PubMed Scopus (29) Google Scholar ), sequenced 12 new genomes, and integrated published citrus genomes including clementine mandarin, pummelo, Mangshan wild mandarin, citron, Ichang papeda, kumquat, Trifoliate orange, and Chinese box orange. Based on the above genomes, we constructed a comprehensive database, named the Citrus Pan-genome to Breeding Database (CPBD), which includes many large-scale datasets of fruit transcriptomes, genome variations, and DNA methylome as well as practical tools for citrus breeding.