ArticleBMC genomics2013
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.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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91 citing papers in PubMed, 174 citations in OpenAlex.
- The Importance of thePlants (Basel, Switzerland) · 2026Review
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Unique structural attributes of the PSI-NDH supercomplex in Physcomitrium patens.The Plant journal : for cell and molecular biology · 2024Article
- Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases.Computational and structural biotechnology journal · 2024Article
- Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.G3 (Bethesda, Md.) · 2024Article
- Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens.Communications biology · 2024Article
- Near telomere-to-telomere genome of the model plant Physcomitrium patens.Nature plants · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens.Nature plants · 2023Article
- A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis.Communications biology · 2023Article
- PEATmoss: A Gene Expression Atlas for Bryophytes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Multiplex CRISPR-Cas9 mutagenesis of the phytochrome gene family in Physcomitrium (Physcomitrella) patens.Plant molecular biology · 2021Article
- Transcriptional profiling reveals conserved and species-specific plant defense responses during the interaction of Physcomitrium patens with Botrytis cinerea.Plant molecular biology · 2021Article
- Expression of a human cDNA in moss results in spliced mRNAs and fragmentary protein isoforms.Communications biology · 2021Article
- A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.Nucleic acids research · 2021Article
- Targeted Gene Knockouts by Protoplast Transformation in the MossFrontiers in genome editing · 2021Review
- The Importance of ATM and ATR inGenes · 2020Article
- Dynamics of the Transcriptome Response to Heat in the Moss, Physcomitrella patens.International journal of molecular sciences · 2020Article
- A NanoFE simulation-based surrogate machine learning model to predict mechanical functionality of protein networks from live confocal imaging.Computational and structural biotechnology journal · 2020Article
- Current Challenges in Studying Alternative Splicing in Plants: The Case ofFrontiers in plant science · 2020Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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