Comparative genomics in conifers

Adaptive convergence can arise when response to selection involves shared molecular or functional mechanisms among multiple taxa. While conifers represent relevant plant models to address this fundamental evolutionary question, comparative genomic studies in this group remain scarce due to the extensive resources needed to overcome the many challenges posed by their large and complex genomes. This study relies on gene SNPs identified in seven eastern North American conifers from the Pinaceae and Cupressaceae families. Transcriptome-wide SNP diversity was highly heterogeneous among species, which likely relates to variations in historical population sizes. Rapidly evolving genes presumed to be under selection were identified and their analysis revealed very limited convergence among taxa. However, convergence increased gradually at the gene family and the biological processes level. From a molecular standpoint, this pattern suggests that each species followed a distinct adaptive trajectory, and that conifers have sufficient metabolic and gene network flexibility to evolve alternative responses to similar selective pressures. Despite a long divergence time of ~350 Mya, we unexpectedly uncovered a set of 20 key genes that are presumably under positive selection in both conifers and Angiosperms, therefore supporting the hypothesis of broader patterns of adaptive convergence among seed plants.