The Institute for Genomic Research Osa1 Rice Genome Annotation Database

Abstract

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.

Differential expression and phylogenetic analysis suggest specialization of plastid-localized members of the PHT4 phosphate transporter family for photosynthetic and heterotrophic tissues

“…The availability of the complete genome sequences for Arabidopsis and rice allowed us to address this issue for two distantly related plant species. We identified seven protein sequences through searches of the TIGR rice genome database (http://rice.tigr.org/) 27 that shared 70-80% similarity to Arabidopsis PHT4 proteins. Iterative searches with the rice sequences revealed no additional homologs, indicating that these seven proteins comprise the rice PHT4 family.…”

Predicting the Size of the Progeny Mapping Population Required to Positionally Clone a Gene

“…The candidate gene resolution (T) ½in kb or gene number, T(kb) or T(gene) was either reported in each study or obtained by personal communication with the authors. In the latter case, these were confirmed by corroborating the kilobase resolution with the gene resolution using the TIGR Pseudomolecules Release 4.0 database (Yuan et al 2005); retroelements, transposons, and transposases were excluded for gene resolution. The calculation of N gametes genotyped was more complex; it required us to distinguish the actual number of progeny genotyped (g) from the number of informative chromosomes (N), defined as chromosomes that had the potential of having a crossover between the target allele and a flanking molecular marker, and where the location of that crossover (proximal or distal to the target) was distinguished (e.g., using progeny testing).…”

Development of intron-flanking EST markers for the Lolium/Festuca complex using rice genomic information

“…Sequence data of ESTs used for primer designs were deposited in DDBJ and Genbank data libraries under accession numbers AB373997 to AB374042. (Yuan et al 2005).…”