An Improved Reference Genome for Physcomitrella

The genome of Physcomitrella patens was the first bryophyte to be sequenced and the first plant genome to be sequenced with whole genome shotgun at the Department of Energy Joint Genome Institute. By virtue of its phylogenetic position, the Physcomitrella genome sequence allows us to infer the genomic composition of the common ancestor of bryophytes and vascular plants and is therefore an invaluable tool for evolutionary developmental studies of land plants. The organism has also become a well-used laboratory model organism as it can be easily grown and transformed.  We have improved the latest Physcomitrella genome sequence as a designated JGI Plant Genome Flagship. The initial genome sequence did not include any long range linking information and lacked chromosome-scale contiguity. For the new version 3 genome sequence, we have added BAC end sequences and constructed a detailed genetic map comprised of 3,695 SNP markers segregating in two haploid populations. We have also rebuilt the genome using our customized Arachne2 pipeline to produce better scaffolding and convert Physcomitrella into a reference sequence on par with the other JGI Plant Flagship genomes.  We will present details on the genetic map construction, additional sequencing, new assembly, pseudomolecule reconstruction and annotation efforts for the reference version 3 Physcomitrella genome.