title: Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics.
abstract: The honey bee is a key pollinator in agricultural operations as well as a model organism for studying the genetics and evolution of social behavior. 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 with 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 ~1500 raw files to search for missing genes and new exons, to revive discarded annotations and to identify over 2000 new coding regions. These results will contribute to a more comprehensive genome annotation and facilitate continued research on this important insect.
authors.affiliation: Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia , 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Alison
authors.initials: A
authors.lastname: McAfee
authors.affiliation: Department of Biology, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
authors.forename: Brock A
authors.initials: BA
authors.lastname: Harpur
authors.affiliation: Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia , 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Sarah
authors.initials: S
authors.lastname: Michaud
authors.affiliation: Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba , 336-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Beavis
authors.affiliation: Department of Biology, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
authors.forename: Clement F
authors.initials: CF
authors.lastname: Kent
authors.affiliation: Department of Biology, York University , 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
authors.forename: Amro
authors.initials: A
authors.lastname: Zayed
authors.affiliation: Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia , 2125 East Mall, Vancouver, British Columbia V6T 1Z4, Canada.
authors.forename: Leonard J
authors.initials: LJ
authors.lastname: Foster
mesh_terms: D000818:Animals; D001516:Bees / Q000235:genetics* / Q000378:metabolism; D049750:Genome, Insect / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D019476:Insect Proteins / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods; D058977:Molecular Sequence Annotation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011499:Protein Processing, Post-Translational; D059748:Proteolysis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods
chemical_list: D019476:Insect Proteins; D020543:Proteome
keywords: Apis mellifera; genome annotation; honey bees; mass spectrometry; proteogenomics