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

Research Article

Tomoaki Nishiyama¹  Stephane Rombauts²  Yves Van de Peer²  Stefan A Rensing³  Mitsuyasu Hasebe⁴  Daniel Lang⁵  Karol Buchta⁵  Andreas D Zimmer⁵  Ralf Reski⁶ 

[1] Advanced Science Research Center, Kanazawa University, Kanazawa, Japan;Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Ghent, Belgium;Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium;Institute of Biology II, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany;BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany;Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany;National Institute for Basic Biology, Okazaki, Japan;School of life Science, The Graduate University for Advanced Studies, 444-8585, Okazaki, Japan;Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany;Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany;BIOSS - Centre for Biological Signalling Studies, Freiburg, Germany;FRIAS - Freiburg Institute for Advanced Studies, Freiburg, Germany;

关键词: Bryophyte;    Physcomitrella patens;    Genome annotation;    Gene structure;    Reference genome;    Model organism;    UTR;    Plant evolution;    Non-flowering plant;    Orphan genes;   

DOI  :  10.1186/1471-2164-14-498

 received in 2013-03-06, accepted in 2013-07-19,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Zimmer et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.