Comparative Analysis of Plastid Genomes Using Pangenome Research ToolKit (PGR-TK)

TL;DR

This study evaluates the Pangenome Research Tool Kit (PGR-TK) for analyzing plastid genomes, demonstrating its ability to recognize structural features and group related species without gene annotations, aiding genome evolution studies.

Contribution

The paper introduces the application of PGR-TK to plastid genomes, showing its effectiveness in structural recognition and species grouping across diverse genera.

Findings

PGR-TK accurately identifies large-scale plastome structures.

The tool groups species from the same genus correctly in cladograms.

It provides insights into genome evolution without gene annotations.

Abstract

Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory analysis investigates whether the Pangenome Research Tool Kit (PGR-TK) is suitable for analyzing plastomes. After determining the optimal parameters for this tool on plastomes, we use it to compare sequences from each of the genera - Magnolia, Solanum, Fragaria and Cotoneaster, as well as a combined set from 20 rosid genera. PGR-TK recognizes large-scale plastome structures, such as the inverted repeats, among combined sequences from distant rosid families. If the plastid genomes are rotated to the same starting point, it also correctly groups different species from the same genus together in a generated cladogram. The visual approach of PGR-TK provides insights into genome evolution without requiring gene annotations.