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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Finding the missing honey bee genes: Lessons learned from a genome upgrade
BMC Genomics, Volume 15, No. 1, Article 86, Year 2014
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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. © 2014 Elsik et al.; licensee BioMed Central Ltd.
Authors & Co-Authors
Elsik, Christine G.
United States, Columbia
University of Missouri
United States, Washington, D.c.
Georgetown University
Worley, Kim Carlyle
United States, Houston
Baylor College of Medicine
Childers, Anna K.
United States, Washington, D.c.
Georgetown University
Beye, Martin
Germany, Dusseldorf
Heinrich-heine-universität Düsseldorf
Câmara, Francisco
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Childers, Christopher P.
United States, Washington, D.c.
Georgetown University
United States, Columbia
University of Missouri
de Graaf, Dirk C.
Belgium, Ghent
Universiteit Gent
Debyser, Griet
Belgium, Ghent
Universiteit Gent
Deng, Jixin
United States, Houston
Baylor College of Medicine
Devreese, Bart V.
Belgium, Ghent
Universiteit Gent
Elhaik, Eran
United States, Baltimore
Johns Hopkins Bloomberg School of Public Health
Evans, Jay D.
United States, Beltsville
Usda Ars Beltsville Agricultural Research Center
Foster, Leonard J.
Canada, Vancouver
The University of British Columbia
Graur, Dan
United States, Houston
University of Houston
Guigó, Roderic
Spain, Barcelona
Universitat Pompeu Fabra Barcelona
Hoff, Katharina J.
Germany, Greifswald
Universität Greifswald
Holder, Michael E.
United States, Houston
Baylor College of Medicine
Hudson, Matthew E.
United States, Urbana
University of Illinois Urbana-champaign
Hunt, Greg J.
United States, West Lafayette
Purdue University
Jiang, Huaiyang
United States, Pittsburgh
University of Pittsburgh School of Medicine
Joshi, Vandita
United States, Houston
Baylor College of Medicine
Khetani, Radhika S.
United States, Urbana
University of Illinois Urbana-champaign
Kosarev, Peter
United States, Mount Kisco
Softberry, Inc.
Kovář, Christie L.
United States, Houston
Baylor College of Medicine
Ma, Jian
United States, Urbana
University of Illinois Urbana-champaign
Maleszka, R.
Australia, Canberra
Anu Research School of Biology
Moritz, Robin F.A.
Germany, Halle
Martin-luther-universität Halle-wittenberg
Muñoz-Torres, Mónica C.
United States, Washington, D.c.
Georgetown University
United States, Berkeley
Lawrence Berkeley National Laboratory
Murphy, Terence D.
United States, Bethesda
National Library of Medicine Nlm
Muzny, Donna Marie
United States, Houston
Baylor College of Medicine
Newsham, Irene F.
United States, Houston
Baylor College of Medicine
Reese, Justin T.
United States, Washington, D.c.
Georgetown University
United States, Columbia
University of Missouri
Robertson, Hugh M.
United States, Urbana
University of Illinois Urbana-champaign
Robinson, Gene E.
United States, Urbana
University of Illinois Urbana-champaign
Rueppell, Olav
United States, Greensboro
The University of North Carolina at Greensboro
Solovyev, Victor V.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Stanke, Mario
Germany, Greifswald
Universität Greifswald
Stolle, Eckart
Germany, Halle
Martin-luther-universität Halle-wittenberg
Tsuruda, Jennifer M.
United States, Clemson
Clemson University
van Vaerenbergh, Matthias
Belgium, Ghent
Universiteit Gent
Waterhouse, Robert M.
Switzerland, Lausanne
Sib Swiss Institute of Bioinformatics
Weaver, Daniel B.
United States, Austin
Genformatic
Whitfield, Charles W.
United States, Urbana
University of Illinois Urbana-champaign
Wu, Yuanqing
United States, Houston
Baylor College of Medicine
Zdobnov, Evgeny M.
Switzerland, Lausanne
Sib Swiss Institute of Bioinformatics
Zhang, Lan
United States, Houston
Baylor College of Medicine
Zhu, Dianhui
United States, Houston
Baylor College of Medicine
Gibbs, Richard A.L.
United States, Houston
Baylor College of Medicine
Patil, Shobha
Unknown Affiliation
Gubbala, S.
Unknown Affiliation
Aqrawi, Peshtewani K.
Unknown Affiliation
Arias, F.
Unknown Affiliation
Bess, C.
Unknown Affiliation
Blankenburg, Kerstin Petra Clerc
Unknown Affiliation
Brocchini, M.
Unknown Affiliation
Buhay, Christian J.
Unknown Affiliation
Challis, Daniel E.
Unknown Affiliation
Chang, Kyle
Unknown Affiliation
Chen, D.
Unknown Affiliation
Coleman, P.
Unknown Affiliation
Drummond, Jennifer A.
Unknown Affiliation
English, A.
Unknown Affiliation
Evani, Uday Shankar
Unknown Affiliation
Francisco, Liezl
Unknown Affiliation
Fu, Qiaomei
Unknown Affiliation
Goodspeed, R.
Unknown Affiliation
Haessly, T. H.
Unknown Affiliation
Hale, Walker
Unknown Affiliation
Han, Hyojun
Unknown Affiliation
Hu, Y.
Unknown Affiliation
Jackson, Laronda
Unknown Affiliation
Jakkamsetti, A.
Unknown Affiliation
Jayaseelan, Joy Christina
Unknown Affiliation
Kakkar, N.
Unknown Affiliation
Kalra, Dinesh K.
Unknown Affiliation
Kandadi, H.
Unknown Affiliation
Lee, Sandra L.
Unknown Affiliation
Li, Haiyan Irene
Unknown Affiliation
Liu, Yan Hu
Unknown Affiliation
Cree, Simone L.
Unknown Affiliation
Mandapat, C. M.
Unknown Affiliation
Mata, Robert
Unknown Affiliation
Mathew, Tittu
Unknown Affiliation
Matskevitch, T.
Unknown Affiliation
Munidasa, M.
Unknown Affiliation
Nagaswamy, U.
Unknown Affiliation
Najjar, R.
Unknown Affiliation
Nguyen, Ngoc Bich
Unknown Affiliation
Niu, Jinzhi
Unknown Affiliation
Opheim, D.
Unknown Affiliation
Palculict, Timothy Blake
Unknown Affiliation
Paul, S.
Unknown Affiliation
Pellon, M.
Unknown Affiliation
Perales, L.
Unknown Affiliation
Pham, Christopher
Unknown Affiliation
Pham, P.
Unknown Affiliation
Pu, Lingling
Unknown Affiliation
Qi, S.
Unknown Affiliation
Qu, Jiaxin
Unknown Affiliation
Ren, Yanru
Unknown Affiliation
Statistics
Citations: 100
Authors: 100
Affiliations: 24
Identifiers
Doi:
10.1186/1471-2164-15-86
e-ISSN:
14712164
Research Areas
Genetics And Genomics