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

Elsik, CG and Worley, KC and Bennett, AK and Beye, M and Camara, F and Childers, CP and de Graaf, DC and Debyser, G and Deng, J and Devreese, B and Elhaik, E and Evans, JD and Foster, LJ and Graur, D and Guigo, R and Hoff, KJ and Holder, ME and Hudson, ME and Hunt, GJ and Jiang, H and Joshi, V and Khetani, RS and Kosarev, P and Kovar, CL and Ma, J and Maleszka, R and Moritz, RFA and Munoz-Torres, MC and Murphy, TD and Muzny, DM and Newsham, IF and Reese, JT and Robertson, HM and Robinson, GE and Rueppell, O and Solovyev, V and Stanke, M and Stolle, E and Tsuruda, JM and Vaerenbergh, MV and Waterhouse, RM and Weaver, DB and Whitfield, CW and Wu, Y and Zdobnov, EM and Zhang, L and Zhu, D and Gibbs, RA and Patil, S and Gubbala, S and Aqrawi, P and Arias, F and Bess, C and Blankenburg, KB and Brocchini, M and Buhay, C and Challis, D and Chang, K and Chen, D and Coleman, P and Drummond, J and English, A and Evani, U and Francisco, L and Fu, Q and Goodspeed, R and Haessly, TH and Hale, W and Han, H and Hu, Y and Jackson, L and Jakkamsetti, A and Jayaseelan, JC and Kakkar, N and Kalra, D and Kandadi, H and Lee, S and Li, H and Liu, Y and Macmil, S and Mandapat, CM and Mata, R and Mathew, T and Matskevitch, T and Munidasa, M and Nagaswamy, U and Najjar, R and Nguyen, N and Niu, J and Opheim, D and Palculict, T and Paul, S and Pellon, M and Perales, L and Pham, C and Pham, P and Pu, LL and Qi, S and Qu, J and Ren, Y (2014) Finding the missing honey bee genes: Lessons learned from a genome upgrade. BMC Genomics, 15 (1).

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Abstract

Background: 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.

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Details

Item Type:	Article
Status:	Published
Creators/Authors:	Creators Email Pitt Username ORCID Elsik, CG Worley, KC Bennett, AK Beye, M Camara, F Childers, CP de Graaf, DC Debyser, G Deng, J Devreese, B Elhaik, E Evans, JD Foster, LJ Graur, D Guigo, R Hoff, KJ Holder, ME Hudson, ME Hunt, GJ Jiang, H HUJ4@pitt.edu HUJ4 Joshi, V Khetani, RS Kosarev, P Kovar, CL Ma, J Maleszka, R Moritz, RFA Munoz-Torres, MC Murphy, TD Muzny, DM Newsham, IF Reese, JT Robertson, HM Robinson, GE Rueppell, O Solovyev, V Stanke, M Stolle, E Tsuruda, JM Vaerenbergh, MV Waterhouse, RM Weaver, DB Whitfield, CW Wu, Y Zdobnov, EM Zhang, L Zhu, D Gibbs, RA Patil, S Gubbala, S Aqrawi, P Arias, F Bess, C Blankenburg, KB Brocchini, M Buhay, C Challis, D Chang, K Chen, D Coleman, P Drummond, J English, A Evani, U Francisco, L Fu, Q Goodspeed, R Haessly, TH Hale, W Han, H Hu, Y Jackson, L Jakkamsetti, A Jayaseelan, JC Kakkar, N Kalra, D Kandadi, H Lee, S Li, H Liu, Y Macmil, S Mandapat, CM Mata, R Mathew, T Matskevitch, T Munidasa, M Nagaswamy, U Najjar, R Nguyen, N Niu, J Opheim, D Palculict, T Paul, S Pellon, M Perales, L Pham, C Pham, P Pu, LL Qi, S Qu, J Ren, Y
Date:	30 January 2014
Date Type:	Publication
Journal or Publication Title:	BMC Genomics
Volume:	15
Number:	1
DOI or Unique Handle:	10.1186/1471-2164-15-86
Schools and Programs:	School of Medicine > Obstetrics, Gynecology, and Reproductive Sciences
Refereed:	Yes
Date Deposited:	02 Dec 2016 20:32
Last Modified:	27 Apr 2019 14:56
URI:	http://d-scholarship.pitt.edu/id/eprint/29606

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