Abstract
BackgroundThe moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usability of a reference genome greatly depends on the quality of the annotation and the availability of centralized community resources. Therefore, in the light of accumulating evidence for missing genes, fragmentary gene structures, false annotations and a low rate of functional annotations on the original release, we decided to improve the moss genome annotation.ResultsHere, we report the complete moss genome re-annotation (designated V1.6) incorporating the increased transcript availability from a multitude of developmental stages and tissue types. We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a central repository for this plant “flagship” genome. The structural annotation of 32,275 protein-coding genes results in 8387 additional loci including 1456 loci with known protein domains or homologs in Plantae. This is the first release to include information on transcript isoforms, suggesting alternative splicing events for at least 10.8% of the loci. Furthermore, this release now also provides information on non-protein-coding loci. Functional annotations were improved regarding quality and coverage, resulting in 58% annotated loci (previously: 41%) that comprise also 7200 additional loci with GO annotations. Access and manual curation of the functional and structural genome annotation is provided via the http://www.cosmoss.org model organism database.ConclusionsComparative analysis of gene structure evolution along the green plant lineage provides novel insights, such as a comparatively high number of loci with 5’-UTR introns in the moss. Comparative analysis of functional annotations reveals expansions of moss house-keeping and metabolic genes and further possibly adaptive, lineage-specific expansions and gains including at least 13% orphan genes.
Highlights
The moss Physcomitrella patens as a model species provides an important reference for earlydiverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies
Improved structural annotation of the P. patens genome The cosmoss.org Physcomitrella patens V1.6 genome annotation reported here is the result of iterative rounds of evidence mapping, repeat masking, gene structure prediction, filtering and model selection and harbors annotation of protein-coding genes, transposable and repetitive elements and, for the first time, definition of non-protein-coding loci
Considering the number of miRNA families, P. patens with 108 families has an intermediate position between the green alga C. reinhardtii (47 families) and the flowering plant A. thaliana (187 families) [51]
Summary
The moss Physcomitrella patens as a model species provides an important reference for earlydiverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The availability of the genomic sequence and the established molecular toolbox provide the ideal foundation for extensive comparative and evo-devo analyses studies This is reflected in the publication record - a growing body of researchers from all fields has begun to apply Physcomitrella as an additional model organism for comparative studies [11,12,13,14,15,16,17,18,19,20]. Large-scale analyses and cross-kingdom comparisons increasingly utilize the moss as a representative organism for the plant kingdom [25,26,27,28,29] This ongoing interest, the available resources, the active community, and the moss’ attractive phylogenetic position recently led the U.S Department of Energy’s Joint Genome Institute (JGI) to select P. patens as a “plant flagship genome” [30]
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