Towards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.

ABSTRACT: The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant aspects of their biology. One troubling trend that emerged from proteomic analyses is that honey bee peptide samples consistently result in lower peptide identification rates compared to other organisms. This suggests that the genome annotation can be improved, or atypical biological processes are interfering with the mass spectrometry workflow. First, we tested whether high levels of polymorphisms could explain some of the missed identifications by searching spectra against the reference proteome (OGSv3.2) versus a customized proteome of a single honey bee, but our results indicate that this contribution was minor. Likewise, error-tolerant peptide searches lead us to eliminate unexpected post-translational modifications as a major factor in missed identifications. We then used a proteogenomic approach with ~1,500 raw files to search for missing genes, new exons, and revive discarded annotations and identified over 2,000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect.

INSTRUMENT(S): Bruker Daltonics micrOTOF series, Q Exactive

ORGANISM(S): Homo Sapiens (human) Caenorhabditis Elegans Saccharomyces Cerevisiae (baker's Yeast) Drosophila Melanogaster (fruit Fly) Apis Mellifera (honeybee) Mus Musculus (mouse)

TISSUE(S): Liver, Whole Body, Cell Culture

SUBMITTER: Alison McAfee  

LAB HEAD: Leonard James Foster

PROVIDER: PXD002275 | Pride | 2016-01-18

REPOSITORIES: Pride