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

Christine G Elsik, Kim C Worley, Anna K Bennett, Martin Beye, Francisco Camara, Christopher P Childers, Dirk C de Graaf, Griet Debyser, Jixin Deng, Bart Devreese, Eran Elhaik, Jay D Evans, Leonard J Foster, Dan Graur, Roderic Guigo, HGSC production teams, Katharina Jasmin Hoff, Michael E Holder, Matthew E Hudson, Greg J Hunt, Huaiyang Jiang, Vandita Joshi, Radhika S Khetani, Peter Kosarev, Christie L Kovar, Jian Ma, Ryszard Maleszka, Robin F A Moritz, Monica C Munoz-Torres, Terence D Murphy, Donna M Muzny, Irene F Newsham, Justin T Reese, Hugh M Robertson, Gene E Robinson, Olav Rueppell, Victor Solovyev, Mario Stanke, Eckart Stolle, Jennifer M Tsuruda, Matthias Van Vaerenbergh, Robert M Waterhouse, Daniel B Weaver, Charles W Whitfield, Yuanqing Wu, Evgeny M Zdobnov, Lan Zhang, Dianhui Zhu, Richard A Gibbs

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.