Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China.
College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi, 030801, China.
BMC Plant Biol. 2023 Apr 27;23(1):223. doi: 10.1186/s12870-023-04238-3.
Foxtail millet (Setaria italica) harbors the small diploid genome (~ 450 Mb) and shows the high inbreeding 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 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.
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 of xiaomi (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 germplasms 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.
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.
黍（Setaria italica）具有小的二倍体基因组（~450 Mb），表现出较高的近亲繁殖率和与几种主要食物、饲料、燃料和生物能源草的密切关系。此前，我们创建了一个类似于拟南芥生活周期的小米 mini 黍。高质量的从头组装基因组数据和高效的农杆菌介导的遗传转化系统使小米成为理想的 C 模式系统。小米 mini 黍已在研究界广泛共享，因此，人们越来越需要一个用户友好的门户和直观的界面来对数据进行探索性分析。
在这里，我们构建了一个 Setaria italica 的多组学数据库（MDSi，http://sky.sxau.edu.cn/MDSi.htm），其中包含小米的基因组注释 161844 个、34436 个编码蛋白的基因及其在 29 种不同小米组织（6 个）和 JG21（23 个）样本中的表达信息，可作为电子荧光图像（xEFP）原位显示。此外，MDSi 还包含 398 份种质的全基因组重测序（WGS）数据，包括 360 份黍和 38 份绿色黍，以及相应的代谢数据。这些种质的 SNPs 和 Indels 已提前调用，并可在交互方式下进行搜索和比较。MDSi 中实现了常见的工具，包括 BLAST、GBrowse、JBrowse、图谱查看器和数据下载。
本研究构建的 MDSi 整合和可视化了基因组学、转录组学和代谢组学三个层面的数据，同时提供了数百份种质资源变异的信息，满足了主流需求，并支持了相应的研究社区。
