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

item ELSIK, CHRISTINE - University Of Missouri
item WORLEY, KIM - Baylor College Of Medicine
item BENNETT, ANNA - University Of Missouri
item BEYE, MARTIN - University Of Missouri
item CAMARA, FRANCISCO - Pompeu Fabra University
item CHILDERS, CHRISTOPHER - University Of Missouri
item DE GRAAF, DIRK - Ghent University
item DEBYSER, GRIET - Ghent University
item DENG, JIXIN - Baylor College Of Medicine
item DEVREESE, BART - Ghent University
item ELHAIK, ERAN - Johns Hopkins School Of Public Health
item Evans, Jay
item FOSTER, LEONARD - University Of British Columbia
item GRAUR, DAN - University Of Houston
item GUIGO, RODERIC - Pompeu Fabra University
item HOFF, KATHARINA - Ernst Moritz Arndt University Of Greifswald
item HOLDER, MICHAEL - Baylor College Of Medicine
item HUDSON, MATTHEW - Ernst Moritz Arndt University Of Greifswald
item HUNT, GREG - Purdue University
item JIANG, HUAIYANG - University Of Pittsburgh
item JOSH, VANDITA - Baylor College Of Medicine
item KHETANI, RADHIKA - University Of Illinois
item KOSAREV, PETER - Softberry Inc
item KOVAR, CHRISTIE - Baylor College Of Medicine
item MA, JIAN - University Of Illinois
item MALESZKA, RYSZARD - Australian National University
item MORITZ, ROBIN - Martin Luther University
item MUNOZ-TORRES, MONICA - Georgetown University
item MURPHY, TERENCE - National Institutes Of Health (NIH)
item MUZNY, DONNA - Baylor College Of Medicine
item NEWSHAM, IRENE - Baylor College Of Medicine
item REESE, JUSTIN - University Of Missouri
item ROBERTSON, HUGH - University Of Illinois
item ROBINSON, GENE - University Of Illinois
item RUEPPELL, OLAV - University Of North Carolina
item SOLOVYEV, VICTOR - King Abdullah University Of Science And Technology
item STANKE, MARIO - Ernst Moritz Arndt University Of Greifswald
item STOLLE, ECKART - Martin Luther University
item TSURUDA, JENNIFER - Purdue University
item VAERENBERGH, MATTHIAS VAN - Ghent University
item WATERHOUSE, ROBERT - University Of Geneva
item WEAVER, DANIEL - Genformatics, Llc
item WHITFIELD, CHARLES - University Of Illinois
item WU, YUANQING - Baylor College Of Medicine
item ZDOBNOV, EVGENY - University Of Geneva
item ZHANG, LAN - Baylor College Of Medicine
item ZHU, DIANHUI - Baylor College Of Medicine
item 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:10.1186/1471-2164-15-86
Citation: 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.