Abstract
Spinach (Spinacia oleracea L.) is a nutritious vegetable enriched with many essential minerals and vitamins. A reference spinach genome has been recently released, and additional spinach genomic resources are being rapidly developed. Therefore, there is an urgent need of a central database to store, query, analyze and integrate various resources of spinach genomic data. To this end, we developed SpinachBase (http://spinachbase.org), which provides centralized public accesses to genomic data as well as analytical tools to assist research and breeding in spinach. The database currently stores the spinach reference genome sequence, and sequences and comprehensive functional annotations of protein-coding genes predicted from the genome. The database also contains gene expression profiles derived from RNA-Seq experiments as well as highly co-expressed genes and genetic variants called from transcriptome sequences of 120 cultivated and wild Spinacia accessions. Biochemical pathways have been predicted from spinach protein-coding genes and are available through a pathway database (SpinachCyc) within SpinachBase. SpinachBase provides a suite of analysis and visualization tools including a genome browser, sequence similarity searches with BLAST, functional enrichment and functional classification analyses and functions to query and retrieve gene sequences and annotations.
Highlights
Spinach (Spinacia oleracea L.) is an economically and nutritionally important vegetable crop belonging to the Amaranthaceae family of Caryophyllales, the basal order of core eudicots [1, 2]
We have developed the SpinachBase, which serves as a central portal for spinach genomic data
The SpinachBase integrates sequences of spinach genome and protein-coding genes, comprehensive functional annotations and biochemical pathways predicted from the protein-coding genes, and analytical tools to assist research and breeding in spinach
Summary
Spinach (Spinacia oleracea L.) is an economically and nutritionally important vegetable crop belonging to the Amaranthaceae family of Caryophyllales, the basal order of core eudicots [1, 2]. Transcriptomes of 120 cultivated and wild Spinacia accessions were sequenced and comparison of these transcriptome sequences has resulted in a large number of variants in the transcribed regions of the spinach genome, as well as a large dataset of gene expression profiles [2, 5]. In SpinachBase, we implemented several extension modules to integrate the comprehensive functional annotation information and RNA-Seq expression profiles, as well as functional enrichment analysis tools.
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