Plastome evolution and phylogenomics of Glycine (Leguminosae: Papilionoideae)

The genus Glycine Willd. is economically important due to the soybean, a major global crop for oil and protein. However, comprehensive phylogenetic studies of this genus are lacking, and plastome evolution remains poorly understood. In this study, we conducted comparative plastomic and phylogenetic analyses using 42 complete Glycine plastomes. This dataset encompassed 28 newly sequenced plastomes, two reassembled from public raw data, and 12 obtained from GenBank, collectively representing 15 of the 29 species in this genus. Comparative analyses revealed these Glycine plastomes range from 152,225 to 152,972 bp in length, and displayed highly conserved quadripartite structure, gene content (111 genes), and collinearity. Nine protein-coding genes and six non-coding regions showed high sequence variability, were thus identified as promising markers for phylogenetics and species delimitation. Selection pressure analyses detected branch-specific positive selection (dN/dS > 1) in rpoB, accD, and rbcL, supporting their potential roles in environmental adaptation. Phylogenomic analyses strongly supported the monophyly of Glycine and its two subgenera (Soja and Glycine), resolving three major clades within subgenus Glycine. However, several species were resolved as non-monophyletic, and the plastomic phylogeny conflicted with nuclear data, indicating cytonuclear discordance likely caused by hybridization, plastid capture, and/or incomplete lineage sorting. These findings highlight the complex evolutionary history of the genus. This study provides the most comprehensive plastome dataset for Glycine to date and offers new insights into its plastome evolution and cytonuclear discordance.