The Physcomitrella patens Flagship Genome Revisited Based on Pseudochromosomes

Following its initial publication, many comparative and evo-devo studies have made use of the Physcomitrella patens genome as a model platform to study land plant evolution. To further improve its utility as reference for non-vascular plant genomes, the Moss Genome Consortium with the JGI at its core has been working to assemble the chromosomes based on SNP-based genotyping and BAC-end sequencing. Last year, V3.0 comprising the 27 chromosomes has been completed and integrated as a pre-release into the Phytozome and cosmoss.org web services.

Utilizing a comprehensive set of NextGen and EST libraries covering various stages of the life cycle and experimental conditions, multiple prediction tools trained on a substantial set of manually curated protein- and non-protein-coding genes, for the last year we have been working on an improved genome annotation V3.1, which will be publicly released along with the publication describing the analysis of the chromosomes.

I will provide the current status and ongoing work within the genome initiative and give an overview of the V3.1 annotation process including the introduction of a novel machine learning based approach for locus definition and model selection not depending on information from specific experimental evidences defining the strand orientation or 5' and 3' ends of transcripts.

V3.1 also provides joined locus definitions and identifiers (CGI; cosmoss gene IDs) for both protein-coding and non-protein coding genes. Further resources that were or are being generated including biocuration, functional annotation, species-specific localization prediction or genome-wide analysis alternative splicing and nonsense-mediated decay will be highlighted.