Advanced

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 and Devreese, Bart , et al. (2014) In BMC Genomics 15.
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... (More)

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.

(Less)
Please use this url to cite or link to this publication:
author
, et al. (More)
(Less)
author collaboration
publishing date
type
Contribution to journal
publication status
published
keywords
Animals, Base Composition, Bees/genetics, Databases, Genetic, Genes, Insect, Interspersed Repetitive Sequences/genetics, Molecular Sequence Annotation, Open Reading Frames/genetics, Peptides/analysis, Sequence Analysis, RNA, Sequence Homology, Amino Acid
in
BMC Genomics
volume
15
article number
86
pages
29 pages
publisher
BioMed Central (BMC)
external identifiers
  • scopus:84896690037
  • pmid:24479613
ISSN
1471-2164
DOI
10.1186/1471-2164-15-86
language
English
LU publication?
no
id
f2f237bc-f084-4968-842e-183882d23d2b
date added to LUP
2019-11-10 16:59:18
date last changed
2020-09-13 07:13:15
@article{f2f237bc-f084-4968-842e-183882d23d2b,
  abstract     = {<p>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.</p><p>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.</p><p>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.</p>},
  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 C 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 F A 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 Vaerenbergh, Matthias Van 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},
  language     = {eng},
  month        = {01},
  publisher    = {BioMed Central (BMC)},
  series       = {BMC Genomics},
  title        = {Finding the missing honey bee genes : lessons learned from a genome upgrade},
  url          = {http://dx.doi.org/10.1186/1471-2164-15-86},
  doi          = {10.1186/1471-2164-15-86},
  volume       = {15},
  year         = {2014},
}