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dc.contributor.authorElsik, Christine G
dc.contributor.authorWorley, Kim C
dc.contributor.authorBennett, Anna K
dc.contributor.authorBeye, Martin
dc.contributor.authorCamara, Francisco
dc.contributor.authorChilders, Christopher P
dc.contributor.authorde Graaf, Dirk C
dc.contributor.authorDebyser, Griet
dc.contributor.authorDeng, Jixin
dc.contributor.authorDevreese, Bart
dc.contributor.authorElhaik, Eran
dc.contributor.authorEvans, Jay D
dc.contributor.authorFoster, Leonard J
dc.contributor.authorGraur, Dan
dc.contributor.authorGuigo, Roderic
dc.contributor.authorHoff, Katharina Jasmin
dc.contributor.authorHolder, Michael E
dc.contributor.authorHudson, Matthew E
dc.contributor.authorHunt, Greg J
dc.contributor.authorJiang, Huaiyang
dc.contributor.authorJoshi, Vandita
dc.contributor.authorKhetani, Radhika S
dc.contributor.authorKosarev, Peter
dc.contributor.authorKovar, Christie L
dc.contributor.authorMa, Jian
dc.contributor.authorMaleszka, Ryszard
dc.contributor.authorMoritz, Robin F A
dc.contributor.authorMunoz-Torres, Monica C
dc.contributor.authorMurphy, Terence D
dc.contributor.authorMuzny, Donna M
dc.contributor.authorNewsham, Irene F
dc.contributor.authorReese, Justin T
dc.contributor.authorRobertson, Hugh M
dc.contributor.authorRobinson, Gene E
dc.contributor.authorRueppell, Olav
dc.contributor.authorSolovyev, Victor
dc.contributor.authorStanke, Mario
dc.contributor.authorStolle, Eckart
dc.contributor.authorTsuruda, Jennifer M
dc.contributor.authorVaerenbergh, Matthias Van
dc.contributor.authorWaterhouse, Robert M
dc.contributor.authorWeaver, Daniel B
dc.contributor.authorWhitfield, Charles W
dc.contributor.authorWu, Yuanqing
dc.contributor.authorZdobnov, Evgeny M
dc.contributor.authorZhang, Lan
dc.contributor.authorZhu, Dianhui
dc.contributor.authorGibbs, Richard A
dc.contributor.authorPatil, S.
dc.contributor.authorGubbala, S.
dc.contributor.authorAqrawi, P.
dc.contributor.authorArias, F.
dc.contributor.authorBess, C.
dc.contributor.authorBlankenburg, K. B.
dc.contributor.authorBrocchini, M.
dc.contributor.authorBuhay, C.
dc.contributor.authorChallis, D.
dc.contributor.authorChang, K.
dc.contributor.authorChen, D.
dc.contributor.authorColeman, P.
dc.contributor.authorDrummond, J.
dc.contributor.authorEnglish, A.
dc.contributor.authorEvani, U.
dc.contributor.authorFrancisco, L.
dc.contributor.authorFu, Q.
dc.contributor.authorGoodspeed, R.
dc.contributor.authorHaessly, T. H.
dc.contributor.authorHale, W.
dc.contributor.authorHan, H.
dc.contributor.authorHu, Y.
dc.contributor.authorJackson, L.
dc.contributor.authorJakkamsetti, A.
dc.contributor.authorJayaseelan, J. C.
dc.contributor.authorKakkar, N.
dc.contributor.authorKalra, D.
dc.contributor.authorKandadi, H.
dc.contributor.authorLee, S.
dc.contributor.authorLi, H.
dc.contributor.authorLiu, Y.
dc.contributor.authorMacmil, S.
dc.contributor.authorMandapat, C. M.
dc.contributor.authorMata, R.
dc.contributor.authorMathew, T.
dc.contributor.authorMatskevitch, T.
dc.contributor.authorMunidasa, M.
dc.contributor.authorNagaswamy, U.
dc.contributor.authorNajjar, R.
dc.contributor.authorNguyen, N.
dc.contributor.authorNiu, J.
dc.contributor.authorOpheim, D.
dc.contributor.authorPalculict, T.
dc.contributor.authorPaul, S.
dc.contributor.authorPellon, M.
dc.contributor.authorPerales, L.
dc.contributor.authorPham, C.
dc.contributor.authorPham, P.
dc.date.accessioned2014-08-27T09:42:08Z
dc.date.available2014-08-27T09:42:08Z
dc.date.issued2014-01-30
dc.identifier.citationElsik CG, Worley KC, Bennett AK, Beye M, Camara F, et al. (2014) Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics 15: 86. doi:10.1186/1471-2164-15-86.
dc.identifier.issn14712164
dc.identifier.pmid24479613
dc.identifier.doi10.1186/1471-2164-15-86
dc.identifier.urihttp://hdl.handle.net/10754/325245
dc.description.abstractBackground: 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.
dc.language.isoen
dc.publisherSpringer Nature
dc.rightsThis 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.
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subjectApis mellifera
dc.subjectGC content
dc.subjectGene annotation
dc.subjectGene prediction
dc.subjectGenome assembly
dc.subjectGenome improvement
dc.subjectGenome sequencing
dc.subjectRepetitive DNA
dc.subjectTranscriptome
dc.subjectcomplementary DNA
dc.subjectcytosine
dc.subjectguanine
dc.subjectRNA
dc.subjectanimal cell
dc.subjectanimal tissue
dc.subjectDNA content
dc.subjectembryo
dc.subjectgenetic code
dc.subjectgenetic resource
dc.subjecthoneybee
dc.subjectinsect genetics
dc.subjectinsect genome
dc.subjectnucleotide sequence
dc.subjectRNA sequence
dc.subjectsequence alignment
dc.subjectsequence analysis
dc.subjectunindexed sequence
dc.subjectHexapoda
dc.subjectMetazoa
dc.titleFinding the missing honey bee genes: Lessons learned from a genome upgrade
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputational Omics Group
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalBMC Genomics
dc.identifier.pmcidPMC4028053
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDivision of Animal Sciences, Division of Plant Sciences and MU Informatics Institute, University of Missouri, Columbia, MO 65211, United States
dc.contributor.institutionDepartment of Biology, Georgetown University, Washington, DC 20057, United States
dc.contributor.institutionHuman Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX 77030, United States
dc.contributor.institutionInstitute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
dc.contributor.institutionCenter for Genomic Regulation, Universitat Pompeu Fabra, C/Dr. Aiguader 88, E-08003 Barcelona, Catalonia, Spain
dc.contributor.institutionDivision of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
dc.contributor.institutionLaboratory of Zoophysiology, Ghent University, Krijgslaan 281 S2, B-9000 Ghent, Belgium
dc.contributor.institutionLaboratory of Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
dc.contributor.institutionDepartment of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205-2103, United States
dc.contributor.institutionBee Research Laboratory, BARC-E, USDA-Agricultural Research Service, Beltsville, MD 20705, United States
dc.contributor.institutionDepartment of Biochemistry and Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada
dc.contributor.institutionDepartment of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, United States
dc.contributor.institutionErnst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
dc.contributor.institutionDepartment of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
dc.contributor.institutionDepartment of Entomology, Purdue University, 901 West State Street, West Lafayette, IN 47907-2089, United States
dc.contributor.institutionDepartment of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, MAGEE 0000, Pittsburgh, PA 15260, United States
dc.contributor.institutionHigh-Performance Biological Computing (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
dc.contributor.institutionSoftberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, United States
dc.contributor.institutionInstitute for Genomic Biology and Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 DCL, MC-278, 1304 W Springfield Ave, Urbana, IL 61801, United States
dc.contributor.institutionResearch School of Biology, The Australian National University, Canberra ACT 0200, Australia
dc.contributor.institutionInstitut fr Zoologie, Molekulare kologie, Martin-Luther-Universitt Halle-Wittenberg, Hoher Weg 4, D-06099 Halle (Saale), Germany
dc.contributor.institutionGenomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
dc.contributor.institutionNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD 20894, United States
dc.contributor.institutionDepartment of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
dc.contributor.institutionInstitute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States
dc.contributor.institutionDepartment of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27412, United States
dc.contributor.institutionExtension Field Operations, Clemson University, 120 McGinty Ct, Clemson, SC 29634, United States
dc.contributor.institutionUniversity of Geneva and Swiss Institute of Bioinformatics, CMU, Michel-Servet 1, Geneva CH-1211, Switzerland
dc.contributor.institutionGenformatic, 6301 Highland Hills Drive, Austin, TX 78731, United States
dc.contributor.institutionDepartment of Entomology, Neuroscience Program, Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personSolovyev, Victor
refterms.dateFOA2018-06-13T14:36:21Z
dc.date.published-online2014-01-30
dc.date.published-print2014


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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.
Except where otherwise noted, this item's license is described as 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.