Advanced search
1 file | 1.30 MB

Finding the missing honey bee genes: lessons learned from a genome upgrade

Author
Organization
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 similar to 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.
Keywords
GC content, Gene prediction, Gene annotation, Apis mellifera, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, OPEN READING FRAMES, APIS-MELLIFERA, TRANSPOSABLE ELEMENTS, CLASSIFICATION-SYSTEM, PROTEIN FAMILIES, DOMAIN DATABASE, TANDEM REPEATS, DNA-SEQUENCES, SOCIAL INSECT, DRAFT GENOME

Downloads

  • Finding the missing honey bee genes 2014 BDV-GD.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 1.30 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Elsik, Christine G, Kim C Worley, Anna K Bennett, Martin Beye, Francisco Camara, Christopher P Childers, Dirk de Graaf, et al. 2014. “Finding the Missing Honey Bee Genes: Lessons Learned from a Genome Upgrade.” Bmc Genomics 15.
APA
Elsik, C. G., Worley, K. C., Bennett, A. K., Beye, M., Camara, F., Childers, C. P., de Graaf, D., et al. (2014). Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC GENOMICS, 15.
Vancouver
1.
Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, et al. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC GENOMICS. 2014;15.
MLA
Elsik, Christine G, Kim C Worley, Anna K Bennett, et al. “Finding the Missing Honey Bee Genes: Lessons Learned from a Genome Upgrade.” BMC GENOMICS 15 (2014): n. pag. Print.
@article{5868309,
  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 similar to 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.},
  articleno    = {86},
  author       = {Elsik, Christine G and Worley, Kim C and Bennett, Anna K and Beye, Martin and Camara, Francisco and Childers, Christopher P and de Graaf, Dirk and Debyser, Griet and Deng, Jixin and Devreese, Bart and Elhaik, Eran and Evans, Jay D and Foster, Leonard J and Graur, Dan and Guigo, Roderic and Hoff, Katharina Jasmin and Holder, Michael E and Hudson, Matthew E and Hunt, Greg J and Jiang, Huaiyang and Joshi, Vandita and Khetani, Radhika S and Kosarev, Peter and Kovar, Christie L and Ma, Jian and Maleszka, Ryszard and Moritz, Robin FA and Munoz-Torres, Monica C and Murphy, Terence D and Muzny, Donna M and Newsham, Irene F and Reese, Justin T and Robertson, Hugh M and Robinson, Gene E and Rueppell, Olav and Solovyev, Victor and Stanke, Mario and Stolle, Eckart and Tsuruda, Jennifer M and Van Vaerenbergh, Matthias and Waterhouse, Robert M and Weaver, Daniel B and Whitfield, Charles W and Wu, Yuanqing and Zdobnov, Evgeny M and Zhang, Lan and Zhu, Dianhui and Gibbs, Richard A},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  language     = {eng},
  pages        = {29},
  title        = {Finding the missing honey bee genes: lessons learned from a genome upgrade},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-86},
  volume       = {15},
  year         = {2014},
}

Altmetric
View in Altmetric
Web of Science
Times cited: