Plant Physiol. Tips for Better Browsing
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
QUICK SEARCH:   [advanced]


     

Plant Physiology Preview
Published on October 19, 2007; 10.1104/pp.107.104513

OPEN ACCESS ARTICLE
This Article
Free via Open Access: OA
Right arrow Full Text (Plant Physiology Preview (PDF))
Right arrow Supplemental Data
Right arrowOA All Versions of this Article:
145/4/1311    most recent
pp.107.104513v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Campbell, M. A.
Right arrow Articles by Buell, C. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Campbell, M. A.
Right arrow Articles by Buell, C. R.
Agricola
Right arrow Articles by Campbell, M. A.
Right arrow Articles by Buell, C. R.

Received June 25, 2007
Accepted October 14, 2007

Identification and Characterization of Lineage-specific Genes within the Poaceae

Matthew A. Campbell , Wei Zhu , Ning Jiang , Haining Lin , Shu Ouyang , Kevin L. Childs , Brian J. Haas , John P. Hamilton , and C. Robin Buell

The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850 and J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA; Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA

Using the Oryza sativa subspecies japonica (rice) genome annotation along with genomic sequence and clustered transcript assemblies from 184 species in the Plant Kingdom, a set of 861 rice genes have been identified that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside of the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed Conserved Poaceae Specific Genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function nor do they contain a functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain containing protein and 4.5% encode a protein with a putative function. On average, the CPSGs have fewer exons, shorter total gene length, and elevated GC content when compared with genes annotated as either transposable elements or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across either a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum and 103 of the 861 rice CPSGs (12.0%) could be made demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for transposable element-related structural characteristics and sequence discounts these CPSGs as being misannotated transposable elements. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as, specific to the Poaceae.






HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
ASPB Publications PLANT PHYSIOLOGY THE PLANT CELL
Copyright © 2007 by the American Society of Plant Biologists