Plastid genome evolution in tribe Desmodieae (Fabaceae: Papilionoideae)

Area of Science:

• Botany
• Genomics
• Evolutionary Biology

Background:

• Legumes (Fabaceae) exhibit diverse plastid genome (plastome) evolution across major clades.
• The tribe Desmodieae, within the systematically complex Phaseoloids, requires further investigation into its plastome evolution and phylogenetic placement.

Purpose of the Study:

• To investigate the plastome evolution of the tribe Desmodieae.
• To analyze the phylogenetic signaling within Desmodieae and its relationship to other Phaseoloid legumes.
• To identify unique genetic markers and structural variations in Desmodieae plastomes.

Main Methods:

• Sequencing of six complete plastomes from Desmodieae and the putative sister genus Mucuna.
• Comparative analysis of gene content, intron presence/absence, and sequence variation (e.g., ycf4).
• Analysis of gene order and phylogenetic reconstruction using plastome-scale data.

Main Results:

• Desmodieae and Mucuna share the loss of the rpl2 intron; Desmodieae uniquely lost the rps12 intron.
• Pseudogenization of ycf4 was specific to the genus Desmodium within Desmodieae.
• A distinct plastome conformation in Desmodieae features an inversion of a trn gene cluster, likely mediated by repeat motif recombination.
• Phylogenetic analysis strongly supports Desmodieae as a monophyletic group nested within the paraphyletic Phaseoleae, with monophyletic subtribes Desmodiinae and Lespedezinae.

Conclusions:

• Plastome data provide significant insights into the evolutionary history and systematic placement of the tribe Desmodieae.
• Unique genetic events and structural rearrangements in Desmodieae plastomes distinguish them within the Phaseoloids.
• The study clarifies the monophyletic nature of Desmodieae and its subtribes, refining legume phylogeny.