Dissecting plant genomes with the PLAZA comparative genomics platform

Area of Science:

• Plant genomics
• Comparative genomics
• Bioinformatics

Background:

• Advancements in next-generation sequencing have led to a surge in publicly available plant genomes.
• This presents both opportunities and challenges for comparative genomics research.
• Efficient tools are needed to explore and analyze this growing genomic data.

Purpose of the Study:

• To present PLAZA 2.5, an updated and user-friendly online research environment for exploring plant genomic information.
• To incorporate newly available plant genomes and enhance existing annotations.
• To introduce new interactive tools and visualizations for comparative genomics analysis.

Main Methods:

• Integration of structural and functional gene annotations for 25 plant species.
• Development of an Integrative Orthology Viewer combining multiple orthology prediction methods.
• Utilizing cross-species expression analysis and phylogenetic profiling.

Main Results:

• PLAZA 2.5 now hosts genomic data for 25 organisms across a broad taxonomic range.
• The Integrative Orthology Viewer facilitates efficient investigation of complex orthology relationships.
• Cross-species expression data integration enhanced the scope of orthology analysis, particularly for distant species.

Conclusions:

• PLAZA 2.5 serves as a valuable resource for comparative plant genomics research.
• The platform's tools and expanded dataset aid in understanding gene families and orthology.
• A proposed set of core gene families can assist in assessing new plant genome assemblies and annotations.