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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

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Bioinformatics: from nucleotids to networks (N2N)
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 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.
Keywords
UTR, Plant evolution, Model organism, Reference genome, Gene structure, Genome annotation, Bryophyte, Physcomitrella patens, Non-flowering plant, Orphan genes, CHLAMYDOMONAS-REINHARDTII, SUBCELLULAR-LOCALIZATION, ARABIDOPSIS-THALIANA, LAND PLANTS, INTRON LOSS, HOMOLOGOUS RECOMBINATION, SPLICE SITES, RNA GENES, MOSS, ANNOTATION

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Citation

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MLA
Zimmer, Andreas D et al. “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.” BMC GENOMICS 14 (2013): n. pag. Print.
APA
Zimmer, A. D., Lang, D., Buchta, K., Rombauts, S., Nishiyama, T., Hasebe, M., Van de Peer, Y., et al. (2013). 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. BMC GENOMICS, 14.
Chicago author-date
Zimmer, Andreas D, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A Rensing, and Ralf Reski. 2013. “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.” Bmc Genomics 14.
Chicago author-date (all authors)
Zimmer, Andreas D, Daniel Lang, Karol Buchta, Stephane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A Rensing, and Ralf Reski. 2013. “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.” Bmc Genomics 14.
Vancouver
1.
Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, et al. 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. BMC GENOMICS. 2013;14.
IEEE
[1]
A. D. Zimmer et al., “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,” BMC GENOMICS, vol. 14, 2013.
@article{4145921,
  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 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.},
  articleno    = {498},
  author       = {Zimmer, Andreas D and Lang, Daniel and Buchta, Karol and Rombauts, Stephane and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Van de Peer, Yves and Rensing, Stefan A and Reski, Ralf},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keywords     = {UTR,Plant evolution,Model organism,Reference genome,Gene structure,Genome annotation,Bryophyte,Physcomitrella patens,Non-flowering plant,Orphan genes,CHLAMYDOMONAS-REINHARDTII,SUBCELLULAR-LOCALIZATION,ARABIDOPSIS-THALIANA,LAND PLANTS,INTRON LOSS,HOMOLOGOUS RECOMBINATION,SPLICE SITES,RNA GENES,MOSS,ANNOTATION},
  language     = {eng},
  pages        = {20},
  title        = {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},
  url          = {http://dx.doi.org/10.1186/1471-2164-14-498},
  volume       = {14},
  year         = {2013},
}

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