We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
IPOP: An Integrative Plant Multi-omics Platform for Cross-species Comparison and Evolutionary Study.
- Authors
Huang, Wenyue; Hu, Xiaona; Ren, Yanlin; Song, Minggui; Ma, Chuang; Miao, Zhenyan
- Abstract
The advent of high-throughput sequencing technologies has led to the production of a significant amount of omics data in plants, which serves as valuable assets for conducting cross-species multi-omics comparative analysis. Nevertheless, the current dearth of comprehensive platforms providing evolutionary annotation information and multi-species multi-omics data impedes users from systematically and efficiently performing evolutionary and functional analysis on specific genes. In order to establish an advanced plant multi-omics platform that provides timely, accurate, and high-caliber omics information, we collected 7 distinct types of omics data from 6 monocots, 6 dicots, and 1 moss, and reanalyzed these data using standardized pipelines. Additionally, we furnished homology information, duplication events, and phylostratigraphic stages of 13 species to facilitate evolutionary examination. Furthermore, the integrative plant omics platform (IPOP) is bundled with a variety of online analysis tools that aid users in conducting evolutionary and functional analysis. Specifically, the Multi-omics Integration Analysis tool is available to consolidate information from diverse omics sources, while the Transcriptome-wide Association Analysis tool facilitates the linkage of functional analysis with phenotype. To illustrate the application of IPOP, we conducted a case study on the YTH domain gene family, wherein we observed shared functionalities within orthologous groups and discerned variations in evolutionary patterns across these groups. To summarize, the IPOP platform offers valuable evolutionary insights and multi-omics data to the plant sciences community, effectively addressing the need for cross-species comparison and evolutionary research platforms. All data and modules within IPOP are freely accessible for academic purposes (http://omicstudio.cloud:4012/ipod/).
- Subjects
MULTIOMICS; BOTANY; FUNCTIONAL analysis; GENE families; NUCLEOTIDE sequencing
- Publication
Molecular Biology & Evolution, 2023, Vol 40, Issue 12, p1
- ISSN
0737-4038
- Publication type
Article
- DOI
10.1093/molbev/msad248