Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions

Abstract

Background: The 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.

Results: Here, 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.

Conclusions: Comparative 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.

Figure 1

A. thaliana best hit (BLASTP) coverage changes from P. patens V1.2 to V1.6 34.5 % of the protein-coding gene models (V1.6) covers better their closest A. thaliana homolog.

Figure 2

Comparison of 5’-UTR intron numbers in Viridiplantae5’-UTR intron number frequencies of selected Viridiplantae genomes. The y-axis labels give the number of transcripts w/o 5’UTR introns in percentage of all transcripts with 5’UTR.

Figure 3

P. patens V1.6 intron lengths distribution 5’-UTR, CDS, and 3’UTR intron lengths in comparison. The percentage of introns longer than 500 bp is much higher in 5’-UTRs than in CDS and 3’-UTR introns.

Figure 4

Distance to translation and transcription start sites of 5’-UTR intron positions Distribution of 5’-UTR positions for P. patens and A. thaliana transcripts in comparison. The closeness of 5’-UTR to the initiating ATG is more pronounced in A. thaliana. While ~75% of introns are closer than 65 bp in A. thaliana only ~50% are in P. patens.

Figure 5

How many moss-specific genes are there? BLAST hits of P. patens-only clusters based on our OrthoMCL clustering with selected Viridiplantae genomes against GenPept (rel. 190). P. patens proteins were excluded from GenPept for this analysis.

Figure 6

Gene family sizes in P. patens proteins from several Viridiplantae were clustered using OrthoMCL. Depicted are all protein clusters with regard to P. patens and sorted by cluster size. The clusters were subdivided into P. patens only clusters and clusters with at least one other member. Protein families found to be expanded in P. patens in comparison to A. thaliana are listed.

Figure 7

Comparison of gene family sizes in conserved clusters distribution of genes per cluster and species common to P. patens and at least one other Viridiplantae (8208 cluster).