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Finding the missing honey bee genes: lessons learned from a genome upgrade
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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028053/ https://www.ncbi.nlm.nih.gov/pubmed/24479613 http://dx.doi.org/10.1186/1471-2164-15-86 |
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author | 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 Jasmin 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 Van Waterhouse, Robert M Weaver, Daniel B Whitfield, Charles W Wu, Yuanqing Zdobnov, Evgeny M Zhang, Lan Zhu, Dianhui Gibbs, Richard A |
author_facet | 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 Jasmin 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 Van Waterhouse, Robert M Weaver, Daniel B Whitfield, Charles W Wu, Yuanqing Zdobnov, Evgeny M Zhang, Lan Zhu, Dianhui Gibbs, Richard A |
author_sort | Elsik, Christine G |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-4028053 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40280532014-05-22 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 Jasmin 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 Van Waterhouse, Robert M Weaver, Daniel B Whitfield, Charles W Wu, Yuanqing Zdobnov, Evgeny M Zhang, Lan Zhu, Dianhui Gibbs, Richard A BMC Genomics Research Article 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. BioMed Central 2014-01-30 /pmc/articles/PMC4028053/ /pubmed/24479613 http://dx.doi.org/10.1186/1471-2164-15-86 Text en Copyright © 2014 Elsik et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article 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 Jasmin 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 Van Waterhouse, Robert M Weaver, Daniel B Whitfield, Charles W Wu, Yuanqing Zdobnov, Evgeny M Zhang, Lan Zhu, Dianhui Gibbs, Richard A Finding the missing honey bee genes: lessons learned from a genome upgrade |
title | Finding the missing honey bee genes: lessons learned from a genome upgrade |
title_full | Finding the missing honey bee genes: lessons learned from a genome upgrade |
title_fullStr | Finding the missing honey bee genes: lessons learned from a genome upgrade |
title_full_unstemmed | Finding the missing honey bee genes: lessons learned from a genome upgrade |
title_short | Finding the missing honey bee genes: lessons learned from a genome upgrade |
title_sort | finding the missing honey bee genes: lessons learned from a genome upgrade |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4028053/ https://www.ncbi.nlm.nih.gov/pubmed/24479613 http://dx.doi.org/10.1186/1471-2164-15-86 |
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