GenomicusPlants: a web resource to study genome evolution in flowering plants

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Comparative genomics and phylogenetic reconstructions are essential for studying gene and genome evolution.
• The increasing volume of genomic data presents challenges for integration and synthesis.
• Existing tools may not fully capture the breadth of evolutionary information.

Purpose of the Study:

• To present GenomicusPlants, a webserver extension for intuitive exploration of flowering plant genomes.
• To facilitate comparative genomics and evolutionary studies across broad evolutionary scales.
• To enable analysis of both extant and ancestral reconstructed plant genomes.

Main Methods:

• Development of GenomicusPlants, an extension of the Genomicus webserver.
• Integration of phylogenetic trees with genomic locus comparisons (PhyloView).
• Visualization of gene order conservation across multiple genomes (AlignView, MatrixView, Karyoview).
• Analysis of 26 extant and 23 ancestral reconstructed flowering plant genomes.

Main Results:

• GenomicusPlants provides four interconnected and customizable views for genomic exploration.
• PhyloView allows cross-genome comparison of genomic loci alongside phylogenetic trees.
• AlignView, MatrixView, and Karyoview offer detailed visualization of gene order and chromosome structure.
• Ancestral gene order data provides a long-term perspective on genome evolution.

Conclusions:

• GenomicusPlants enhances the interrogation, integration, and synthesis of comparative plant genomic data.
• The tool supports evolutionary studies by providing intuitive access to diverse genomic information.
• Facilitates understanding of gene and genome evolution in flowering plants across evolutionary timescales.