The Ceratodon purpureus transcriptome ushers in the era of moss comparative genomics

Abstract

This chapter outlines the scope of the ongoing Ceratodon purpureus genome project and provides an overview of the C. purpureus transcriptome, the evolution of the C. purpureus UV sex chromosomes, and the patterns of polymorphism in the species. Comparative analyses of the transcriptomes of a male and a female isolate showed that C. purpureus and the moss model Physcomitrella patens had highly overlapping gene sets, and that most of the genes shared between these two species evolve under strong purifying selection. However, the differences between the C. purpureus and P. patens genomes refined our understanding of the timing of gene family gain and loss across the land plants and the heterogeneity in rate of molecular evolution across the genome of these two species. Ceratodon purpureus showed a slightly greater codon usage bias compared to P. patens, which may be explained by the contrasting mating system of the two species. The C. purpureus transcriptomes also showed evidence of a genome doubling event ∼65–76 MYA that was independent of the contemporaneous polyploidy event inferred for P. patens. These data also suggested considerable physiological and developmental divergence between the two species. Genetic mapping and molecular evolutionary analysis showed that the nonrecombining UV chromosomes of C. purpureus are actively capturing new genes, illustrating that at least this part of the genome is highly dynamic. Moreover, patterns of polymorphism were highly variable across the genome, suggesting that sexual recombination in other parts of the genome decouples even genes on the same chromosome, and they experience different patterns of natural selection. The forthcoming C. purpureus genome will build on these existing resources and enable us to answer definitively many questions regarding the evolution of land plant gene families, genome structure, and the genetic basis of adaptive variation.