The MSU Rice Genome Annotation Project

The MSU Rice Genome Annotation Project (http://rice.plantbiology.msu.edu) provides high quality annotation of the rice genome to the international rice research community. The rice pseudomolecules for the current annotation (Release 7) have been reconstructed using an optical-map based optimal BAC tiling path as well as error correction of the underlying BAC sequences using next generation sequencing reads from Nipponbare rice. This effort, in collaboration with researchers at the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan and the Rice Annotation Project Database (RAP-DB), represents a final and unified set of pseudomolecules (Os-Nipponbare-Reference-IRGSP-1.0).  The pseudomolecules have been annotated with numerous data types which can be viewed on the Genome Browser:  FGENESH models, SSRs, rice genetic markers, expression array probes, MPSS and SAGE tags, rice EST and FL-cDNA alignments,16 RNA-Seq wiggle tracks, SNPs from the OryzaSNP project, and alignments of transcript data from 23 additional plant species. Each gene model on the genome browser is linked to a gene report page that displays Plant GOSlim assignments, PFAM domain matches, InterPro Matches, UniRef100 BLASTP matches, gene associations, Orthologous Group membership and RNA-Seq Expression values from 16 RNA-Seq libraries.  Original gene models were created using a combination of ab initio gene predictions and alignment evidence.  Gene models have been assigned putative functional descriptions based on protein sequence similarities with Genbank's non-redundant database and with Pfam domain alignments. Orthologous gene groups have been predicted using genes from rice, sorghum, Arabidopsis, poplar, grapevine, Brachypodium, and maize. All data from the project are available on our website (http://rice.plantbiology.msu.edu).