The Beginnings of Bryophyte Comparative Genomics: The Transcriptome of Ceratodon purpureus

The moss Ceratodon purpureus has long served as a model system in several areas of developmental biology and evolutionary genetics. The Department of Energy Joint Genome Institute has begun sequencing both a male (R40) and a female (GG1) laboratory isolate of the species. The sequence data currently available include transcriptomes of the R40 and GG1 isolates from early developmental tissues (protonema) under standard and hormone treated conditions. In addition, a BAC library was constructed for GG1. Whole genome shotgun sequencing is planned for this isolate, and resequencing is planned for R40. We have also generated a mapping population between GG1 and R40. Together these resources will be employed to construct the first version of the C. purpureus genome.

C. purpureus will be the second moss genome, after P. patens, to be completely sequenced, and this effort will pave the way for a moss comparative genomics research program. We anticipate that this program will have several important outcomes for our understanding of several major research areas, in particular the evolution of gene content and genome structure across the land plants, the evolution of sex chromosomes, and the genetic basis of complex traits. Here we use the transcriptomic data to provide a preliminary analysis of evolutionary divergence from the P. patens reference genome and a survey of polymorphism between R40 and GG1. We also present an analysis of genetic variation on the sex chromosomes of C. purpureus from a population sample and show that these chromosomes have recently acquired several genes.