MDSi: Multi-omics Database for Setaria italica

文献类型： 外文期刊

第一作者： Li, Xukai

作者： Li, Xukai;Hou, Siyu;Han, Yuanhuai;Gao, Jianhua;Wang, Xingchun;Li, Xukai;Feng, Mengmeng;Gao, Jianhua;Wang, Xingchun;Hou, Siyu;Han, Yuanhuai;Xia, Rui;Li, Jiawei;Tang, Sha

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关键词： Database; Multi-omics; Foxtail millet; Setaria italica; Tools

期刊名称：BMC PLANT BIOLOGY （ 影响因子：5.3； 五年影响因子：5.9 ）

ISSN： 1471-2229

年卷期： 2023 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Background Foxtail millet (Setaria italica) harbors the small diploid genome (similar to 450 Mb) and shows the high inbreed-ing rate and close relationship to several major foods, feed, fuel and bioenergy grasses. Previously, we created a mini foxtail millet, xiaomi, with an Arabidopsis-like life cycle. The de novo assembled genome data with high-quality and an efficient Agrobacterium-mediated genetic transformation system made xiaomi an ideal C-4 model system. The mini foxtail millet has been widely shared in the research community and as a result there is a growing need for a user-friendly portal and intuitive interface to perform exploratory analysis of the data. Results Here, we built a Multi-omics Database for Setaria italica (MDSi, http://sky.sxau.edu.cn/MDSi.htm), that contains xiaomi genome of 161,844 annotations, 34,436 protein-coding genes and their expression information in 29 different tissues ofxiaomi (6) and JG21 (23) samples that can be showed as an Electronic Fluorescent Pictograph (xEFP) in-situ. Moreover, the whole-genome resequencing (WGS) data of 398 germplasms, including 360 foxtail millets and 38 green foxtails and the corresponding metabolic data were available in MDSi. The SNPs and Indels of these germ-plasms were called in advance and can be searched and compared in an interactive manner. Common tools including BLAST, GBrowse, JBrowse, map viewer, and data downloads were implemented in MDSi. Conclusion The MDSi constructed in this study integrated and visualized data from three levels of genomics, transcriptomics and metabolomics, and also provides information on the variation of hundreds of germplasm resources that can satisfies the mainstream requirements and supports the corresponding research community.

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