Abstract
Sesame is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America. Upon the completion of the sesame reference genome version 1.0, we launched Sinbase 1.0 as an integrated database for genomic and bioinformatics analyses. Recently, an upgraded version (version 2.0) of the genome sequence was released. In addition, large numbers of multi-omics data have been generated on sesame, but a comprehensive database that integrates these resources for the community has been lacking until now. Here, we developed an interactive and comprehensive sesame multi-omics database, Sinbase 2.0, which provides information of the sesame updated genome containing 13 chromosomes, 3 genetic linkage maps, 5 intra- and 6 inter-species comparative genomics, 1 genomic variation analysis, 5 transcriptome data, 1 proteome, 31 functional markers, 175 putative functional genes, and 54 QTLs detected for important agronomic traits. Moreover, Sinbase 2.0 has been enriched with novel user-friendly computational tools. All datasets of Sinbase 2.0 can be downloaded online conveniently. Sinbase 2.0 will be updated regularly with new available sesame multi-omics data and can be accessed freely via Sinbase 2.—Sesame Muti-Omics Database. We expect that Sinbase 2.0, similarly to the previous version, will continue to make a major contribution to advance sesame research towards a better understanding of its biology and genetic improvement, as well as comparative genomics and evolutionary biology.
Highlights
Sesame (Sesamum indicum L., 2n = 26) is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America [1,2].Sesame becomes a prized cash crop for small-scale farmers in developing countries because of its low production costs and high sale price
Contents and Functions nomics; proteomics; and functional markers, genes geand quantitative trait locus (QTL) using In Sinbase 2.0, we transcriptomics; integrated sesame updated genomics; genetics; comparative multiple-layer methods according to different multi-omics data formats
Sinbase 1.0 was the first practical and integrated database that focuses on the S. indicum genomics, genetics, and comparative genomics with its relatives and other important species in the plant community
Summary
The development of high-throughput sequencing technologies has promoted the study of sesame biology, generating invaluable multi-omics data. As sesame is gradually graduating from an “orphan crop” to a “genomic resource-rich crop”, several multi-omics data have been generated recently [3]. The transcriptome data of sesame plants following drought stress and recovering periods was generated [8]. Another important abiotic stress was investigated by Wang et al (2016) who reported large gene expression data under waterlogging stress in two contrasting sesame genotypes [9]. (http://www.sesame-bioinfo.org/Sinbase2.0), which provides information of the sesame updated genome (version 2.0), genetic linkage maps, comparative genomics, genomic variation, transcriptomics, proteomics, functional markers, genes, and QTLs. Sinbase2.0 supplies user-friendly visualized and searchable tools, which can help users to retrieve sesame multi-omics information
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