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Title:   Author  item
                                            ELSIK, CHRISTINE - University Of Missouriitem
                                            WORLEY, KIM - Baylor College Of Medicineitem
                                            BENNETT, ANNA - University Of Missouriitem
                                            BEYE, MARTIN - University Of Missouriitem
                                            CAMARA, FRANCISCO - Pompeu Fabra Universityitem
                                            CHILDERS, CHRISTOPHER - University Of Missouriitem
                                            DE GRAAF, DIRK - Ghent Universityitem
                                            DEBYSER, GRIET - Ghent Universityitem
                                            DENG, JIXIN - Baylor College Of Medicineitem
                                            DEVREESE, BART - Ghent Universityitem
                                            ELHAIK, ERAN - Johns Hopkins School Of Public Healthitem
                                            Evans, Jayitem
                                            FOSTER, LEONARD - University Of British Columbiaitem
                                            GRAUR, DAN - University Of Houstonitem
                                            GUIGO, RODERIC - Pompeu Fabra Universityitem
                                            HOFF, KATHARINA - Ernst Moritz Arndt University Of Greifswalditem
                                            HOLDER, MICHAEL - Baylor College Of Medicineitem
                                            HUDSON, MATTHEW - Ernst Moritz Arndt University Of Greifswalditem
                                            HUNT, GREG - Purdue Universityitem
                                            JIANG, HUAIYANG - University Of Pittsburghitem
                                            JOSH, VANDITA - Baylor College Of Medicineitem
                                            KHETANI, RADHIKA - University Of Illinoisitem
                                            KOSAREV, PETER - Softberry Incitem
                                            KOVAR, CHRISTIE - Baylor College Of Medicineitem
                                            MA, JIAN - University Of Illinoisitem
                                            MALESZKA, RYSZARD - Australian National Universityitem
                                            MORITZ, ROBIN - Martin Luther Universityitem
                                            MUNOZ-TORRES, MONICA - Georgetown Universityitem
                                            MURPHY, TERENCE - National Institutes Of Health (NIH)item
                                            MUZNY, DONNA - Baylor College Of Medicineitem
                                            NEWSHAM, IRENE - Baylor College Of Medicineitem
                                            REESE, JUSTIN - University Of Missouriitem
                                            ROBERTSON, HUGH - University Of Illinoisitem
                                            ROBINSON, GENE - University Of Illinoisitem
                                            RUEPPELL, OLAV - University Of North Carolinaitem
                                            SOLOVYEV, VICTOR - King Abdullah University Of Science And Technologyitem
                                            STANKE, MARIO - Ernst Moritz Arndt University Of Greifswalditem
                                            STOLLE, ECKART - Martin Luther Universityitem
                                            TSURUDA, JENNIFER - Purdue Universityitem
                                            VAERENBERGH, MATTHIAS VAN - Ghent Universityitem
                                            WATERHOUSE, ROBERT - University Of Genevaitem
                                            WEAVER, DANIEL - Genformatics,  Llcitem
                                            WHITFIELD, CHARLES - University Of Illinoisitem
                                            WU, YUANQING - Baylor College Of Medicineitem
                                            ZDOBNOV, EVGENY - University Of Genevaitem
                                            ZHANG, LAN - Baylor College Of Medicineitem
                                            ZHU, DIANHUI - Baylor College Of Medicineitem
                                            GIBBS, RICHARD - Baylor College Of Medicine
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 1/27/2014
                                    Publication  Date: 1/30/2014
                                    Publication URL: http://doi:10.1186/1471-2164-15-86Citation: Elsik, C.G., Worley, K.C., Bennett, A.K., Beye, M., Camara, F.C., Childers, C.P., De Graaf, D.C., Debyser, G., Deng, J., Devreese, B., Elhaik, E., Evans, J.D., Foster, L.J., Graur, D., Guigo, R., Hoff, K.J., Holder, M.E., Hudson, M.E., Hunt, G.J., Jiang, H., Josh, V., Khetani, R.S., Kosarev, P., Kovar, C.L., Ma, J., Maleszka, R., Moritz, R.F., Munoz-Torres, M.C., Murphy, T.D., Muzny, D.M., Newsham, I.F., Reese, J.T., Robertson, H.M., Robinson, G.E., Rueppell, O., Solovyev, V., Stanke, M., Stolle, E., Tsuruda, J.M., Vaerenbergh, M., Waterhouse, R.M., Weaver, D.B., Whitfield, C.W., Wu, Y., Zdobnov, E.M., Zhang, L., Zhu, D., Gibbs, R.A. 2014. Finding the missing honey bee genes: lessons learned from a genome upgrade. Biomed Central (BMC) Genomics. 15:86.Interpretive Summary: Honey bees are a vital pollinator of many of the world’s crops and provide important hive resources for agriculture at many levels. The honey bee genome is being used to breed better bees, and to better understand the impacts of nutritional, parasite, and chemical stress on bees. These insights will lead to better bee management, and regulation of bee risks, leading to a more sustainable bee supply for agriculture. This paper describes an extensive update of the honey bee genome project, giving better insights into bee biology and management.
                                Technical Abstract: 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. 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. 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.


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