On October 30th, the internationally renowned journal Nucleic Acids Research (Impact Factor 11.147) published online the latest research findings on the construction of the functional genomics database of Malvaceae plants co-finished by Professor Zhou Yu and Academician Zhu Yuxian from the College of Life Sciences. This has provided a powerful online analytical tool for botanists to conduct comparative genomics analysis of Malvaceae plants.
The paper is entitled MaGenDB: a functional genomics hub for Malvaceae plants. Wang Dehe, Fan Weiliang and Guo Xiaolong, doctoral students from the College of Life Sciences, are co-first authors. Professor Zhou Yu, Academician Zhu Yuxian and Associate Professor Wang Kun are co-corresponding authors. The work is funded by National Natural Science Foundation of China, Ministry of Science and Technology, and independent research and interdisciplinary research programs of Wuhan University.
Malvaceae is an important branch of the botany, including many significant economic crops, such as cotton and jute from seed and stem fiber, cocoa bean for cocoa and chocolate candy, durian honored as tropic “king of the fruits”, ornamental flower plant hibiscus and linden tree, a source of fine wood. The in-depth analysis of the genomics of the Malvaceae plants and the accumulating high-throughput data like transcriptional regulation urge researchers to produce a multi-layer data comparison tool for integrating genome, epigenetic modifications, transcriptome, and proteome, which can also compare and analyze the specific biological processes of plant-specific families or the gene sequences, structures, and transcriptional regulation of gene families.
Therefore, Zhou Yu, Zhu Yuxian, Wang Kun and some other experts jointly established the first functional genomics of Malvaceae plants website — MaGenDB (http://magen.whu.edu.cn). Up to now, MaGenDB has included a total of 13 species of 9 genera of Malvaceae and corresponding information of genome-wide association studies sites (GWAS), and single nucleotide variation sites (SNV). Also, it has comprised and processed the total 374 sets of 9 sorts of constitutive data, including RNA-seq and protein profiles, predicted and identified 24.85 million different types of functional elements, 28.97 million gene collinear relationships, and 170 million protein-protein interaction pairs. Moreover, the database independently designed and developed various visual components and genome online comparison tools, and can provide user-friendly data retrieval, download and online analysis services through organically integrating different types of data with the effective association.
This is another vital research finding of the two research teams, following the recent publication of the fine transcriptome map of Asian cotton in Nature Communications.
The construction and functions of MaGenDB
Rewritten by: Dong Xiaoqian, edited by Caosiyi, Shen Yuxi and Hu Siji
