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

BMC Genomics

Research Article

Jay D Evans¹  Roderic Guigo²  Francisco Camara²  Victor Solovyev³  Leonard J Foster⁴  Dan Graur⁵  Anna K Bennett⁶  Justin T Reese⁷  Christopher P Childers⁷  Monica C Munoz-Torres⁸  Olav Rueppell⁹  Matthew E Hudson^1,10  Charles W Whitfield^1,11  Greg J Hunt^1,12  Hugh M Robertson^1,13  Eran Elhaik^1,14  Huaiyang Jiang^1,15  Christine G Elsik^1,16  Katharina Jasmin Hoff^1,17  Mario Stanke^1,17  Jennifer M Tsuruda^1,18  Daniel B Weaver^1,19  Radhika S Khetani^2,20  Kim C Worley^2,21  Vandita Joshi^2,21  Jixin Deng^2,21  Yuanqing Wu^2,21  Richard A Gibbs^2,21  Lan Zhang^2,21  Michael E Holder^2,21  Dianhui Zhu^2,21  Donna M Muzny^2,21  Christie L Kovar^2,21  Irene F Newsham^2,21  Robin F A Moritz^2,22  Eckart Stolle^2,22  Jian Ma^2,23  Gene E Robinson^2,24  Martin Beye^2,25  Bart Devreese^2,26  Griet Debyser^2,26  Dirk C de Graaf^2,27  Matthias Van Vaerenbergh^2,27  Terence D Murphy^2,28  Ryszard Maleszka^2,29  Peter Kosarev^3,30  Evgeny M Zdobnov^3,31  Robert M Waterhouse^3,31 

[1] Bee Research Laboratory, BARC-E, USDA-Agricultural Research Service, 20705, Beltsville, MD, USA;Center for Genomic Regulation, Universitat Pompeu Fabra, C/Dr. Aiguader 88, E-08003, Barcelona, Catalonia, Spain;Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia;Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada;Department of Biology and Biochemistry, University of Houston, 77204-5001, Houston, TX, USA;Department of Biology, Georgetown University, 20057, Washington, DC, USA;Department of Biology, Georgetown University, 20057, Washington, DC, USA;Division of Animal Sciences, University of Missouri, 65211, Columbia, MO, USA;Department of Biology, Georgetown University, 20057, Washington, DC, USA;Genomics Division, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA;Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, 27412, Greensboro, NC, USA;Department of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;Department of Entomology, Neuroscience Program, Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;Department of Entomology, Purdue University, 901 West State Street, 47907-2089, West Lafayette, IN, USA;Department of Entomology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, 21205-2103, Baltimore, MD, USA;Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, MAGEE 0000, 15260, Pittsburgh, PA, USA;Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, 65211, Columbia, MO, USA;Department of Biology, Georgetown University, 20057, Washington, DC, USA;Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany;Extension Field Operations, Clemson University, 120 McGinty Ct, 29634, Clemson, SC, USA;Genformatic, 6301 Highland Hills Drive, 78731, Austin, TX, USA;High-Performance Biological Computing (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA;Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, 77030, Houston, TX, USA;Institut für Zoologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, D-06099, Halle (Saale), Germany;Institute for Genomic Biology and Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 DCL, MC-278, 1304 W Springfield Ave, 61801, Urbana, IL, USA;Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, 61801, Urbana, IL, USA;Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany;Laboratory of Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium;Laboratory of Zoophysiology, Ghent University, Krijgslaan 281 S2, B-9000, Ghent, Belgium;National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, 20894, Bethesda, MD, USA;Research School of Biology, The Australian National University, ACT 0200, Canberra, Australia;Softberry Inc., 116 Radio Circle, Suite 400, 10549, Mount Kisco, NY, USA;University of Geneva and Swiss Institute of Bioinformatics, CMU, Michel-Servet 1, CH-1211, Geneva, Switzerland;

关键词: Apis mellifera;    GC content;    Gene annotation;    Gene prediction;    Genome assembly;    Genome improvement;    Genome sequencing;    Repetitive DNA;    Transcriptome;   

DOI  :  10.1186/1471-2164-15-86

 received in 2013-09-11, accepted in 2014-01-27,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsHere, 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.ConclusionsLessons 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.

【 授权许可】

CC BY   
© Elsik et al.; licensee BioMed Central Ltd. 2014