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

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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.




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