MaGenDB: a functional genomics hub for Malvaceae plants

作者:Wang, DH (Wang, Dehe)[ 1,2 ] ; Fan, WL (Fan, Weiliang)[ 1 ] ; Guo, XL (Guo, Xiaolong)[ 1,2 ] ; Wu, K (Wu, Kai)[ 1,2 ] ; Zhou, SY (Zhou, Siyu)[ 3 ] ; Chen, ZG (Chen, Zonggui)[ 4 ] ; Li, DY (Li, Danyang)[ 1 ] ; Wang, K (Wang, Kun)[ 1 ] ; Zhu, YX (Zhu, Yuxian)[ 1,4 ] ; Zhou, Y (Zhou, Yu)[ 1,2,4 ]

NUCLEIC ACIDS RESEARCH

卷: 48 期: D1 页: D1076-D1084

DOI: 10.1093/nar/gkz953

出版年:JAN 8 2020

文献类型:Article

摘要

Malvaceae is a family of flowering plants containing many economically important plant species including cotton, cacao and durian. Recently, the genomes of several Malvaceae species have been decoded, and many omics data were generated for individual species. However, no integrative database of multiple species, enabling users to jointly compare and analyse relevant data, is available for Malvaceae. Thus, we developed a user-friendly database named MaGenDB (http://magen.whu.edu.cn) as a functional genomics hub for the plant community. We collected the genomes of 13 Malvaceae species, and comprehensively annotated genes from different perspectives including functional RNA/protein element, gene ontology, KEGG orthology, and gene family. We processed 374 sets of diverse omics data with the ENCODE pipelines and integrated them into a customised genome browser, and designed multiple dynamic charts to present gene/RNA/protein-level knowledge such as dynamic expression profiles and functional elements. We also implemented a smart search system for efficiently mining genes. In addition, we constructed a functional comparison system to help comparative analysis between genes on multiple features in one species or across closely related species. This database and associated tools will allow users to quickly retrieve large-scale functional information for biological discovery.

关键词

KeyWords Plus:DRAFT GENOME; RESOURCE; SEQUENCE; EVOLUTIONARY; SEARCH

作者信息

通讯作者地址:

Wuhan University Wuhan Univ, Coll Life Sci, Wuhan 430072, Peoples R China.

Wuhan University Wuhan Univ, State Key Lab Virol, Wuhan 430072, Peoples R China.

Wuhan University Wuhan Univ, Inst Adv Studies, Wuhan 430072, Peoples R China.

通讯作者地址: Wang, K; Zhu, YX; Zhou, Y (通讯作者)

Wuhan Univ, Coll Life Sci, Wuhan 430072, Peoples R China.

通讯作者地址: Zhou, Y (通讯作者)

Wuhan Univ, State Key Lab Virol, Wuhan 430072, Peoples R China.

通讯作者地址: Zhu, YX; Zhou, Y (通讯作者)

Wuhan Univ, Inst Adv Studies, Wuhan 430072, Peoples R China.

地址:

[ 1 ]‎ Wuhan Univ, Coll Life Sci, Wuhan 430072, Peoples R China

[ 2 ]‎ Wuhan Univ, State Key Lab Virol, Wuhan 430072, Peoples R China

[ 3 ]‎ Hunan Univ, Coll Informat Sci & Engn, Changsha 410082, Peoples R China

[ 4 ]‎ Wuhan Univ, Inst Adv Studies, Wuhan 430072, Peoples R China

电子邮件地址:wangk05@whu.edu.cn; zhuyx@whu.edu.cn; yu.zhou@whu.edu.cn