Li Zhidong, Li Ying, Liu Tongkun, Zhang Changwei, Xiao Dong, Hou Xilin
State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P. R. China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crop, Ministry of Education of the P. R. China, College of Horticulture, Nanjing Agricultural University, Nanjing Suman Plasma Engineering Research Institute, Nanjing 210095, China.
Plants (Basel). 2022 Apr 7;11(8):1005. doi: 10.3390/plants11081005.
The availability of a high-quality genome sequence of ssp. NHCC001 has paved the way for deep mining of genome data. We used the NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding.
不结球白菜亚种NHCC001高质量基因组序列的获得为深入挖掘基因组数据铺平了道路。我们利用NHCC001基因组草图开发了一个综合数据库，即不结球白菜数据库，该数据库提供对NHCC001基因组数据的访问。该数据库提供了127,347个简单序列重复（SSR），从中设计了382,041对引物。NHCCDB包含105,360个基因的信息，这些基因进一步被分类到63个转录因子家族中。此外，NHCCDB提供了八种用于生物学或测序数据分析的工具，包括序列比对工具、功能基因组学工具、比较基因组学工具、基序分析工具、基因组浏览器、引物设计和SSR分析工具。此外，使用NHCCDB可以快速生成八种图形，包括箱线图、维恩图、相关系数图、Q-Q图、曼哈顿图、序列标志图、火山图和热图。我们在NHCCDB中纳入了一个用于高效挖掘转录因子和基因的搜索系统以及一个嵌入式数据提交功能。我们相信NHCCDB数据库将成为不结球白菜研究和育种的一个有用平台。
