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Finding the missing honey bee genes: lessons learned from a genome upgrade Elsik, Christine G.; Worley, Kim C.; Bennett, Anna K.; Beye, Martin; Camara, Francisco; Childers, Christopher P.; de Graaf, Dirk C.; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D.; Foster, Leonard J.; Graur, Dan; Guigo, Roderic; Hoff, Katharina J.; Holder, Michael E.; Hudson, Matthew E.; Hunt, Greg J.; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S.; Kosarev, Peter; Kovar, Christie L.; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F. A.; Munoz-Torres, Monica C.; Murphy, Terence D.; Muzny, Donna M.; Newsham, Irene F.; Reese, Justin T.; Robertson, Hugh M.; Robinson, Gene E.; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M.; Vaerenbergh, Matthias V.; Waterhouse, Robert M.; Weaver, Daniel B.; Whitfield, Charles W.; Wu, Yuanqing; Zdobnov, Evgeny M.; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A.

Abstract

Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

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Title
Finding the missing honey bee genes: lessons learned from a genome upgrade
Creator
Elsik, Christine G.; Worley, Kim C.; Bennett, Anna K.; Beye, Martin; Camara, Francisco; Childers, Christopher P.; de Graaf, Dirk C.; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D.; Foster, Leonard J.; Graur, Dan; Guigo, Roderic; Hoff, Katharina J.; Holder, Michael E.; Hudson, Matthew E.; Hunt, Greg J.; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S.; Kosarev, Peter; Kovar, Christie L.; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F. A.; Munoz-Torres, Monica C.; Murphy, Terence D.; Muzny, Donna M.; Newsham, Irene F.; Reese, Justin T.; Robertson, Hugh M.; Robinson, Gene E.; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M.; Vaerenbergh, Matthias V.; Waterhouse, Robert M.; Weaver, Daniel B.; Whitfield, Charles W.; Wu, Yuanqing; Zdobnov, Evgeny M.; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A.
Publisher
BioMed Central
Date Issued
2014-01-30
Description
Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Genre
Article
Type
Text
Language
eng
Date Available
2016-07-26
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0307140
URI
http://hdl.handle.net/2429/58553
Affiliation
Medicine, Faculty of; Non UBC; Biochemistry and Molecular Biology, Department of
Citation
BMC Genomics. 2014 Jan 30;15(1):86
Publisher DOI
10.1186/1471-2164-15-86
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
Elsik et al.; licensee BioMed Central Ltd.
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)