AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research

Area of Science:

• Plant genomics
• Bioinformatics
• Systems biology

Background:

• The Asteraceae family is a large dicotyledon group with significant economic and medicinal importance.
• Advancements in genomics and transcriptomics generate vast amounts of data for Asteraceae species.
• Existing databases lack efficient gene mining and cross-species study capabilities.

Purpose of the Study:

• To develop a comprehensive multi-omics information resource for the Asteraceae plant community.
• To address limitations in current databases for functional gene mining and comparative genomics.
• To create a centralized platform for integrating and analyzing diverse omics data in Asteraceae.

Main Methods:

• Integration of multi-omics data from 74 Asteraceae species, including genomes, transcriptomes, variants, and metabolites.
• Development of the Asteraceae Multi-omics Information Resource (AMIR) as a centralized data hub.
• Implementation of pan-genome, comparative genomics, and transcriptome systems within AMIR.
• Inclusion of user-friendly bioinformatics tools for customized data analysis.

Main Results:

• AMIR integrates data from 132 genomes, 4,408,432 gene annotations, 3,897 transcriptome samples, 42,765,290 variants, and 15,662 metabolite genes.
• Establishment of the first pan-genome, comparative genomics, and transcriptome system for Asteraceae.
• Demonstration of AMIR's capability for rapid, reproducible, and reliable bioinformatics analyses through case studies.
• Provision of user-friendly tools for customized analysis of Asteraceae multi-omics data.

Conclusions:

• AMIR significantly advances functional genomics research in Asteraceae by integrating multi-omics data.
• The platform facilitates efficient data mining and cross-species comparative studies.
• AMIR supports and enhances breeding practices for economically important Asteraceae crops and medicinal herbs.
• This resource empowers the Asteraceae research community with integrated data and analytical tools.