Rice genome IRGSP-1.0 has now 5 annotation tracks
With our colleagues from KAUST and other organizations, we are preparing the new publication on the analysis of 18 reference genomes from the “Rice Platinum Standard”. The pre-print has been submitted to bioRxiv (Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa) | bioRxiv). As a part of the submission, we are publishing gene annotation tracks for all of the 18 rice genomes. We have added two more gene model tracks to the popular IRGSP-1.0 rice assembly. So, if the three tracks that existed before have not been enough, we now have five annotation tracks with models predicted by Gnomon (NCBI), MSU, FGENESH, Gramene, and CSHL.
While the gene models from the different tracks have something in common, still, every method gives its own set of genes. To resolve the discrepancy, use the RNA-seq tracks and decide which exon structure is more accurate and is consistent with the expressed regions.