Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae)

Area of Science:

• Plant genomics
• Evolutionary biology
• Forest ecology

Background:

• The genus Lithocarpus is ecologically significant in East Asian forests, but its plastome structure and evolution are poorly understood.
• This study addresses the knowledge gap by analyzing 34 Lithocarpus plastomes, including 21 newly assembled ones.

Purpose of the Study:

• To comprehensively analyze the plastome structure and evolutionary patterns of the genus Lithocarpus.
• To reconstruct a phylogenomic tree to reveal maternal evolutionary history.
• To investigate potential drivers of adaptation and cytonuclear discordance.

Main Methods:

• Sequencing and assembly of 34 Lithocarpus plastomes.
• Phylogenomic analysis to reconstruct evolutionary relationships.
• Comparative genomic analysis to identify gene variations and selection pressures.

Main Results:

• Lithocarpus plastomes are typically quadripartite, with conserved gene content but significant variability in SSRs and SC/IR boundary regions.
• The infA gene is identified as a pseudogene in 17 species, and four genes (accD, atpF, rpl32, rps8) show evidence of positive selection.
• Plastome-based phylogeny strongly supports Lithocarpus monophyly but differs from nuclear genome-based phylogenies, indicating cytonuclear discordance.

Conclusions:

• Genes involved in metabolism, photosynthesis, and energy in Lithocarpus are under positive selection, likely due to environmental adaptation.
• The phylogeny suggests limited seed-mediated gene flow in the ancestral lineage.
• Cytonuclear discordance in Lithocarpus and other Fagaceae may result from ancient introgression, incomplete lineage sorting, and asymmetrical gene flow.