CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW
TL;DR
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Abstract
The Brassicaceae family is important both scientifically and economically; however, its complex evolutionary history, characterized by rapid diversification, whole-genome duplications, and significant reticular evolution, makes its classification challenging. The advent of high-throughput next-generation sequencing technology has facilitated the shift from single-locus phylogenomics to whole-plastome phylogenomics, improving our understanding of the family's deep evolutionary relationships. This comprehensive review reinforces our understanding of Brassicaceae chloroplast genomes, highlighting the highly consistent gene content, distinctive base composition patterns, and highly conserved quadruple structure. Phylogenetically relevant structural changes, including temporal shifts in the boundaries of inverted repeats (IRs), lineage-specific gene losses (e.g., rps16), and the loss of ndh genes in response to local adaptive pressures, are investigated in this study. Furthermore, the effectiveness of plastid phylogenics in clarifying taxonomically complex clades was evaluated, while directly addressing common problems such as cytonuclear incompatibility, chloroplast capture, and soft polytomies at key backbone nodes. The article examined newly developed methodologies, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction. Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.