The Drosophila pseudoobscura genome sequence has been updated to the release 3 assembly produced by the HGSC group at Baylor School of Medicine. New methods were employed as described here that combined PacBio sequencing information with the release 2 genome assembly to resolve and improve gaps in the assembly. The annotations from FlyBase release 2.30 have been migrated to the new assembly as annotation release 3.1.

Due to the nature of the assembly improvement the large majority of existing annotations were transferred to the new assembly with updated genome coordinates but no changes to the structure of their annotations models. For approximately 900 transcript models the size of the introns changed due to gap filling but the exons remained the same and there were no changes in coding potential of these models. We were not able to automatically migrate 72 existing gene models as they had spanned or extended into gaps in release 2 that had been removed in release 3. FlyBase curators manually examined and adjusted models for these cases as needed. This resulted in 10 annotations being deleted because they were either duplicated fragments of existing annotations or low-complexity repeat sequences. In addition, two existing release 2 annotations were merged into a corrected release 3 annotation. The migrated annotations are being submitted to GenBank and we will post a news item when the new annotations and assembly are available from NCBI.

De novo nucleotide and protein alignments to the release 3 genome will be generated by NCBI and will be added as Gbrowse tracks once they become available. Brian Oliver's group is working to remap their RNAseq data to the new assembly and we plan to incorporate the remapped data into our Gbrowse views once it is available. We suggest that you refer to the archived FB2013_01 FlyBase release to view the existing RNAseq data on the release 2 assembly in the mean time.