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

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• 作者：Christine G Elsik (1) (2)
  Kim C Worley (3)
  Anna K Bennett (2)
  Martin Beye (4)
  Francisco Camara (5)
  Christopher P Childers (2) (6)
  Dirk C de Graaf (7)
  Griet Debyser (8)
  Jixin Deng (3)
  Bart Devreese (8)
  Eran Elhaik (9)
  Jay D Evans (10)
  Leonard J Foster (11)
  Dan Graur (12)
  Roderic Guigo (5)
  Katharina Jasmin Hoff (13)
  Michael E Holder (3)
  Matthew E Hudson (14)
  Greg J Hunt (15)
  Huaiyang Jiang (16)
  Vandita Joshi (3)
  Radhika S Khetani (17)
  Peter Kosarev (18)
  Christie L Kovar (3)
  Jian Ma (19)
  Ryszard Maleszka (20)
  Robin F A Moritz (21)
  Monica C Munoz-Torres (2) (22)
  Terence D Murphy (23)
  Donna M Muzny (3)
  Irene F Newsham (3)
  Justin T Reese (2) (6)
  Hugh M Robertson (24)
  Gene E Robinson (25)
  Olav Rueppell (26)
  Victor Solovyev (27)
  Mario Stanke (13)
  Eckart Stolle (21)
  Jennifer M Tsuruda (28)
  Matthias Van Vaerenbergh (7)
  Robert M Waterhouse (29)
  Daniel B Weaver (30)
  Charles W Whitfield (31)
  Yuanqing Wu (3)
  Evgeny M Zdobnov (29)
  Lan Zhang (3)
  Dianhui Zhu (3)
  Richard A Gibbs (3)
  
• 关键词：Apis mellifera ; GC content ; Gene annotation ; Gene prediction ; Genome assembly ; Genome improvement ; Genome sequencing ; Repetitive DNA ; Transcriptome
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,007 KB
• 作者单位：Christine G Elsik (1) (2)
  Kim C Worley (3)
  Anna K Bennett (2)
  Martin Beye (4)
  Francisco Camara (5)
  Christopher P Childers (2) (6)
  Dirk C de Graaf (7)
  Griet Debyser (8)
  Jixin Deng (3)
  Bart Devreese (8)
  Eran Elhaik (9)
  Jay D Evans (10)
  Leonard J Foster (11)
  Dan Graur (12)
  Roderic Guigo (5)
  Katharina Jasmin Hoff (13)
  Michael E Holder (3)
  Matthew E Hudson (14)
  Greg J Hunt (15)
  Huaiyang Jiang (16)
  Vandita Joshi (3)
  Radhika S Khetani (17)
  Peter Kosarev (18)
  Christie L Kovar (3)
  Jian Ma (19)
  Ryszard Maleszka (20)
  Robin F A Moritz (21)
  Monica C Munoz-Torres (2) (22)
  Terence D Murphy (23)
  Donna M Muzny (3)
  Irene F Newsham (3)
  Justin T Reese (2) (6)
  Hugh M Robertson (24)
  Gene E Robinson (25)
  Olav Rueppell (26)
  Victor Solovyev (27)
  Mario Stanke (13)
  Eckart Stolle (21)
  Jennifer M Tsuruda (28)
  Matthias Van Vaerenbergh (7)
  Robert M Waterhouse (29)
  Daniel B Weaver (30)
  Charles W Whitfield (31)
  Yuanqing Wu (3)
  Evgeny M Zdobnov (29)
  Lan Zhang (3)
  Dianhui Zhu (3)
  Richard A Gibbs (3)
  
  1. Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
  2. Department of Biology, Georgetown University, Washington, DC, 20057, USA
  3. Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA
  4. Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
  5. Center for Genomic Regulation, Universitat Pompeu Fabra, C/Dr. Aiguader 88, E-08003, Barcelona, Catalonia, Spain
  6. Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
  7. Laboratory of Zoophysiology, Ghent University, Krijgslaan, 281 S2, B-9000, Ghent, Belgium
  8. Laboratory of Protein Biochemistry and Biomolecular Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000, Ghent, Belgium
  9. Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205-2103, USA
  10. Bee Research Laboratory, BARC-E, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
  11. Department of Biochemistry & Molecular Biology, Centre for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC, Canada
  12. Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
  13. Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
  14. Department of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  15. Department of Entomology, Purdue University, 901 West State Street, West Lafayette, IN, 47907-2089, USA
  16. Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, MAGEE 0000, Pittsburgh, PA, 15260, USA
  17. High-Performance Biological Computing (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  18. Softberry Inc, 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
  19. Institute for Genomic Biology and Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 DCL, MC-278, 1304 W Springfield Ave, Urbana, IL, 61801, USA
  20. Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
  21. Institut f眉r Zoologie, Molekulare 脰kologie, Martin-Luther-Universit盲t Halle-Wittenberg, Hoher Weg 4, D-06099, Halle (Saale), Germany
  22. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
  23. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD, 20894, USA
  24. Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  25. Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
  26. Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27412, USA
  27. Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
  28. Extension Field Operations, Clemson University, 120 McGinty Ct, Clemson, SC, 29634, USA
  29. University of Geneva and Swiss Institute of Bioinformatics, CMU, Michel-Servet 1, Geneva, CH-1211, Switzerland
  30. Genformatic, 6301 Highland Hills Drive, Austin, TX, 78731, USA
  31. Department of Entomology, Neuroscience Program, Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
  
• ISSN：1471-2164

文摘

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.