文献类型： 外文期刊

作者： Yang, Xue-Dong ¹ ; Tan, Hua-Wei ² ; Zhu, Wei-Min ¹ ;

作者机构： 1.Shanghai Acad Agr Sci, Protected Hort Inst, Shanghai, Peoples R China

2.Nanjing Agr Univ, Coll Hort, Nanjing, Jiangsu, Peoples R China

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2016 年 11 卷 5 期

页码：

收录情况： SCI

摘要： 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.