title: Identification and characterization of pseudogenes in the rice gene complement.
abstract: BACKGROUND
  The Osa1 Genome Annotation of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. As such, it is likely to mis-annotate pseudogenes as functional genes. A total of 22,033 gene models within the Osa1 Release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, or, for genes residing within a segmentally duplicated region, lack of a paralog or significantly shorter corresponding paralog.
  
  
  RESULTS
  A total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. Significant difference in the length of duplicated genes within segmentally-duplicated regions was the optimal indicator of pseudogenization. Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events. A total of 12% of the pseudogenes were expressed. Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes.
  
  
  CONCLUSIONS
  These pseudogenes still have a detectable open reading frame and are thus distinct from pseudogenes detected within intergenic regions which typically lack definable open reading frames. Families containing the highest number of pseudogenes are fast-evolving families involved in ubiquitination and secondary metabolism.
authors.affiliation: The J. Craig Venter Institute, 9712 Medical Center Dr, Rockville, MD 20850, USA. thibaudf@ncbi.nlm.nih.gov
authors.forename: Françoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.forename: Shu
authors.initials: S
authors.lastname: Ouyang
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics*; D011544:Pseudogenes; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant