Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Area of Science:

• Evolutionary Biology
• Genomics
• Botany

Background:

• Maples (Acer) are ecologically vital and diverse trees, but previous phylogenetic studies using plastid markers lacked resolution, leaving deep evolutionary relationships unclear.
• Understanding maple evolution is crucial due to their economic and ecological importance in north-temperate forests.

Purpose of the Study:

• To generate and analyze plastid genome sequences from 16 maple species to improve phylogenetic resolution within the genus Acer.
• To identify variable regions and potential molecular markers for genetic and phylogenetic studies in maples.

Main Methods:

• Sequencing of 16 maple species' plastid genomes.
• Analysis of repeated sequences, codon usage, and variable regions within the plastomes.
• Phylogenetic analyses using Maximum Likelihood (ML) and Bayesian methods with partitioned datasets.

Main Results:

• Plastomes ranged from 155,212 to 157,023 bp; Acer palmatum showed structural variations.
• Two genes (rps2, rpl22) may be non-functional in several species.
• Fifteen highly variable loci and SSRs were identified in non-coding regions, suitable for molecular markers.
• Plastome-based phylogeny resolved deep relationships but conflicted with a recent nuclear tree, suggesting potential hybridization.

Conclusions:

• Plastid genome sequences are powerful tools for resolving deep-level evolutionary relationships in the genus Acer.
• Identified variable loci and SSRs will aid in developing markers for ecological and evolutionary studies.
• The discordance with the nuclear tree highlights the need for further research into maple diversification, including hybridization.