Representation and High‐Quality Annotation of the Physcomitrella patens Transcriptome Demonstrates a High Proportion of Proteins Involved in Metabolism in Mosses

Abstract

To gain insight into the transcriptome of the well-used plant model system Physcomitrella patens, several EST sequencing projects have been undertaken. We have clustered, assembled, and annotated all publicly available EST and CDS sequences in order to represent the transcriptome of this non-seed plant. Here, we present our fully annotated knowledge resource for the Physcomitrella patens transcriptome, integrating annotation from the production process of the clustered sequences and from a high-quality annotation pipeline developed during this study. Each transcript is represented as an entity containing full annotations and GO term associations. The whole production, filtering, clustering, and annotation process is being modelled and results in seven datasets, representing the annotated Physcomitrella transcriptome from different perspectives. We were able to annotate 63.4 % of the 26 123 virtual transcripts. The transcript archetype, as covered by our clustered data, is compared to a compilation based on all available Physcomitrella full length CDS. The distribution of the gene ontology annotations (GOA) for the virtual transcriptome of Physcomitrella patens demonstrates consistency in the ratios of the core molecular functions among the plant GOA. However, the metabolism subcategory is over-represented in bryophytes as compared to seed plants. This observation can be taken as an indicator for the wealth of alternative metabolic pathways in moss in comparison to spermatophytes. All resources presented in this study have been made available to the scientific community through a suite of user-friendly web interfaces via www.cosmoss.org and form the basis for assembly and annotation of the moss genome, which will be sequenced in 2005.

Targeted knock‐out of a gene encoding sulfite reductase in the moss Physcomitrella patens affects gametophytic and sporophytic development

“…Many such analyses revealed an unexpected variety of enzymes and pathways alternative to those in flowering plants. These observations were corroborated by transcriptome analysis which showed that, whereas in seed plants 10-44% of genes are involved in metabolism, the proportion of metabolic genes in P. patens reaches 70-80% [21]. Analysis of sulfur metabolism in P. patens revealed that some metabolic steps are less complex in this moss than in seed plants, while others are more diverse in mosses [19].…”

Can mosses serve as model organisms for forest research?

“…Considering the absence of a second allele which could balance somatic mutations, this drawback is compensated by a high metabolic redundancy (Lang et al 2005), whole genome duplications (Rensing et al 2007), and the arrest of the cell cycle after DNA synthesis in the G2 phase (Schween et al 2003), combined with efficient DNA repair mechanisms such as homologous recombination (Kamisugi et al 2006). …”

The moss Physcomitrella patens: methods and tools from cultivation to targeted analysis of gene function

“…Thereby, the selection of genes of interest that will be disrupted is based on bioinformatic predictions or experimental indications. Nevertheless, as approximately 1/3 of the P. patens transcripts do not show significant homology to genes from other species (Nishiyama et al, 2003;Lang et al, 2005), there is a particular demand for unbiased forward genetics screens to determine novel gene functions.…”