SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach

• Published in: PloS one 2016-05, Vol.11 (5), p.e0152706-e0152706
• Main Authors: Yang, Xue-Dong, Tan, Hua-Wei, Zhu, Wei-Min
• Format: Article
• Language: English
• Subjects: Amaranthaceae; Arabidopsis; Biology and Life Sciences; Classification; Cultivars; Data mining; Databases, Genetic; Downloading; Gene expression; Gene Expression Profiling; Genes; Genes, Plant; Genetic engineering; Genetics; Genomes; Genomics; Germplasm; Horticulture; Identification; Polymorphism, Single Nucleotide; Proteins; Research and Analysis Methods; Researchers; Ribonucleic acid; RNA; Single-nucleotide polymorphism; Spinach; Spinacia oleracea; Spinacia oleracea - genetics; Studies; Sugar beet; Sugar beets; Transcription factors; Vegetables; Vitaceae; Web sites
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0152706

Spinach (Spinacia oleracea L.), which originated in central and western Asia, belongs to the family Amaranthaceae. Spinach is one of most important leafy vegetables with a high nutritional value as well as being a perfect research material for plant sex chromosome models. As the completion of genome assembly and gene prediction of spinach, we developed SpinachDB (http://222.73.98.124/spinachdb) to store, annotate, mine and analyze genomics and genetics datasets efficiently. In this study, all of 21702 spinach genes were annotated. A total of 15741 spinach genes were catalogued into 4351 families, including identification of a substantial number of transcription factors. To construct a high-density genetic map, a total of 131592 SSRs and 1125743 potential SNPs located in 548801 loci of spinach genome were identified in 11 cultivated and wild spinach cultivars. The expression profiles were also performed with RNA-seq data using the FPKM method, which could be used to compare the genes. Paralogs in spinach and the orthologous genes in Arabidopsis, grape, sugar beet and rice were identified for comparative genome analysis. Finally, the SpinachDB website contains seven main sections, including the homepage; the GBrowse map that integrates genome, genes, SSR and SNP marker information; the Blast alignment service; the gene family classification search tool; the orthologous and paralogous gene pairs search tool; and the download and useful contact information. SpinachDB will be continually expanded to include newly generated robust genomics and genetics data sets along with the associated data mining and analysis tools.