Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics

被引:18
作者
McAfee, Alison [1 ]
Harpur, Brock A. [2 ]
Michaud, Sarah [1 ,4 ]
Beavis, Ronald C. [3 ]
Kent, Clement F. [2 ]
Zayed, Amro [2 ]
Fostert, Leonard J. [1 ]
机构
[1] Univ British Columbia, Ctr High Throughput Biol, Dept Biochem & Mol Biol, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada
[2] York Univ, Dept Biol, 4700 Keele St, Toronto, ON M3J 1P3, Canada
[3] Univ Manitoba, Dept Biochem & Med Genet, Fac Hlth Sci, 336-745 Bannatyne Ave, Winnipeg, MB R3E 0J9, Canada
[4] Univ Victoria, Genome BC Prote Ctr, 4464 Markham St, Victoria, BC V8Z 7X8, Canada
基金
加拿大自然科学与工程研究理事会; 加拿大创新基金会;
关键词
honey bees; Apis mellifera; genome annotation; mass spectrometry; proteogenomics; MASS-SPECTROMETRY; SHOTGUN PROTEOMICS; PESTICIDE-RESIDUES; PROTEIN EXPRESSION; WORKER; IDENTIFICATION; GENES; QUANTIFICATION; EMBRYOGENESIS; RECOMBINATION;
D O I
10.1021/acs.jproteome.5b00589
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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 similar to 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.
引用
收藏
页码:411 / 421
页数:11
相关论文
共 50 条
[41]   Neonicotinoid insecticides in pollen, honey and adult bees in colonies of the European honey bee (Apis mellifera L.) in Egypt [J].
Codling, Garry ;
Al Naggar, Yahya ;
Giesy, John P. ;
Robertson, Albert J. .
ECOTOXICOLOGY, 2018, 27 (02) :122-131
[42]   Neonicotinoid insecticides in pollen, honey and adult bees in colonies of the European honey bee (Apis mellifera L.) in Egypt [J].
Garry Codling ;
Yahya Al Naggar ;
John P. Giesy ;
Albert J. Robertson .
Ecotoxicology, 2018, 27 :122-131
[43]   Effect of the bacterium Paenibacillus larvae larvae on vitellogenin gene expression of the queen honey bee Apis mellifera L. [J].
Gomaa, S. A. S. ;
Barakat, E. M. S. ;
Salama, M. S. ;
El-Gohary, E. E. .
AFRICAN ENTOMOLOGY, 2021, 29 (01) :96-103
[44]   Regulation of the brain dopaminergic system by juvenile hormone in honey bee males (Apis mellifera L.) [J].
Sasaki, K. ;
Akasaka, S. ;
Mezawa, R. ;
Shimada, K. ;
Maekawa, K. .
INSECT MOLECULAR BIOLOGY, 2012, 21 (05) :502-509
[45]   The presence of chronic bee paralysis virus infection in honey bees (Apis mellifera L.) in the USA [J].
Chen, Yan Ping ;
Evans, Jay D. ;
Pettis, Jeff S. .
JOURNAL OF APICULTURAL RESEARCH, 2011, 50 (01) :85-86
[46]   Dietary phytochemicals alter hypopharyngeal gland size in honey bee (Apis mellifera L.) workers [J].
Nino, Elina L. ;
Yokota, Seiji ;
Stacy, William H. O. ;
Arathi, H. S. .
HELIYON, 2022, 8 (09)
[47]   Pollen foraging behaviour of honey bee (Apis mellifera L.) in southern West Bengal, India [J].
Layek, Ujjwal ;
Manna, Siddhartha S. ;
Karmakar, Prakash .
PALYNOLOGY, 2020, 44 (01) :114-126
[48]   Effects of honey bee (Apis mellifera L.) queen insemination volume on worker behavior and physiology [J].
Nino, Elina L. ;
Malka, Osnat ;
Hefetz, Abraham ;
Teal, Peter ;
Hayes, Jerry ;
Grozinger, Christina M. .
JOURNAL OF INSECT PHYSIOLOGY, 2012, 58 (08) :1082-1089
[49]   Morphometric and genetic variability of honey bee (Apis mellifera L.) populations from northern Iran [J].
Kence, Meral ;
Farhoud, Houmen Jabbari ;
Tunca, Rahsan Ivgin .
JOURNAL OF APICULTURAL RESEARCH, 2009, 48 (04) :247-255
[50]   Morphological and molecular characterization of the Landes honey bee (Apis mellifera L.) ecotype for genetic conservation [J].
Strange, James P. ;
Garnery, Lionel ;
Sheppard, Walter S. .
JOURNAL OF INSECT CONSERVATION, 2008, 12 (05) :527-537