Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

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• 作者：Leif Andersson (1) (2)
  Alan L Archibald (3)
  Cynthia D Bottema (4)
  Rudiger Brauning (5)
  Shane C Burgess (6)
  Dave W Burt (3)
  Eduardo Casas (7)
  Hans H Cheng (8)
  Laura Clarke (9)
  Christine Couldrey (10)
  Brian P Dalrymple (11)
  Christine G Elsik (12)
  Sylvain Foissac (13)
  Elisabetta Giuffra (14)
  Martien A Groenen (15)
  Ben J Hayes (16) (17) (18)
  LuSheng S Huang (19)
  Hassan Khatib (20)
  James W Kijas (11)
  Heebal Kim (21)
  Joan K Lunney (22)
  Fiona M McCarthy (23)
  John C McEwan (24)
  Stephen Moore (25)
  Bindu Nanduri (26)
  Cedric Notredame (27)
  Yniv Palti (28)
  Graham S Plastow (29)
  James M Reecy (30)
  Gary A Rohrer (31)
  Elena Sarropoulou (32)
  Carl J Schmidt (33)
  Jeffrey Silverstein (34)
  Ross L Tellam (35)
  Michele Tixier-Boichard (14)
  Gwenola Tosser-Klopp (13)
  Christopher K Tuggle (30)
  Johanna Vilkki (36)
  Stephen N White (37) (38)
  Shuhong Zhao (39)
  Huaijun Zhou (40)
  The FAANG Consortium
  
  1. Science for Life Laboratory Uppsala ; Department of Medical Biochemistry and Microbiology ; Uppsala University ; Uppsala ; SE 751 23 ; Sweden
  2. Department of Animal Breeding and Genetics ; Swedish University of Agricultural Sciences ; Uppsala ; SE-750 07 ; Sweden
  3. The Roslin Institute and Royal (Dick) School of Veterinary Studies ; University of Edinburgh ; Edinburgh ; EH25 9RG ; UK
  4. School of Animal and Veterinary Sciences ; The University of Adelaide ; Roseworthy ; SA ; 5371 ; Australia
  5. Invermay Agricultural Centre ; AgResearch Limited ; Mosgiel ; 9053 ; New Zealand
  6. College of Agriculture and Life Sciences ; University of Arizona ; Tucson ; AZ ; 85719 ; USA
  7. National Animal Disease Center ; United States Department of Agriculture ; Agricultural Research Service ; Ames ; IA ; 50010 ; USA
  8. Avian Disease and Oncology Laboratory ; United States Department of Agriculture ; Agricultural Research Service ; East Lansing ; MI ; 48823 ; USA
  9. European Molecular Biology Laboratory European Bioinformatics Institute ; Hinxton ; Cambridge ; CB10 1SD ; UK
  10. Livestock Improvement Corporation ; Hamilton ; 3284 ; New Zealand
  11. Agriculture Flagship ; Commonwealth Scientific and Industrial Research Organisation ; St Lucia ; 4067 ; Brisbane ; Australia
  12. Division of Animal Sciences ; University of Missouri ; Columbia ; MO ; 65211 ; USA
  13. UMR1388 G茅n茅tique ; Physiologie et Syst猫mes d鈥橢levage (GenPhySE) ; French National Institute for Agricultural Research (INRA) ; F-31326 ; Castanet-Tolosan ; France
  14. UMR1313 G茅n茅tique Animale et Biologie Int茅grative (GABI) ; French National Institute for Agricultural Research (INRA) ; F-78352 ; Jouy-en-Josas ; France
  15. Animal Breeding and Genomics Centre ; Wageningen University ; 6708聽PB ; Wageningen ; The Netherlands
  16. Biosciences Research Division ; Department of Environment and Primary Industries Victoria ; Bundoora ; 3083 ; Australia
  17. Dairy Futures Cooperative Research Centre ; Bundoora ; 3083 ; VIC ; Australia
  18. La Trobe University ; Bundoora ; 3086 ; VIC ; Australia
  19. Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China ; Jiangxi Agricultural University ; Jiangxi ; 330029 ; People鈥檚 Republic of China
  20. Department of Animal Sciences ; University of Wisconsin-Madison ; Madison ; WI ; 53706 ; USA
  21. Department of Agricultural Biotechnology ; Seoul National University ; Seoul ; Republic of Korea
  22. Animal Parasitic Diseases Laboratory ; United States Department of Agriculture ; Agricultural Research Service ; Beltsville ; MD ; 20705 ; USA
  23. School of Animal and Comparative Biomedical Sciences ; University of Arizona ; Tucson ; AZ ; 85721 ; USA
  24. Animal Productivity Group ; AgResearch Limited ; Mosgiel ; 9053 ; New Zealand
  25. Centre for Animal Science ; Queensland Alliance for Agriculture & Food Innovation ; University of Queensland ; St Lucia ; QLD ; 4067 ; Australia
  26. Department of Basic Sciences ; College of Veterinary Medicine and Institute for Genomics ; Biocomputing and Biotechnology ; Mississippi State University ; Mississippi ; MS ; 39762 ; USA
  27. Comparative Bioinformatics ; Centre for Genomic Regulation (CRG) ; Dr. Aiguader 88 ; 08003 ; Barcelona ; Spain
  28. National Center for Cool and Cold Water Aquaculture ; United States Department of Agriculture ; Agricultural Research Service ; Kearneysville ; WV ; 25430 ; USA
  29. Livestock Gentec Centre ; Department of Agricultural ; Food and Nutritional Science ; University of Alberta ; Edmonton ; Alberta ; T6G 2C8 ; Canada
  30. Department of Animal Science ; Iowa State University ; Ames ; IA ; 50011 ; USA
  31. US Meat Animal Research Center ; United States Department of Agriculture ; Agricultural Research Service ; Clay Center ; NE ; 68933 ; USA
  32. Institute of Marine Biology ; Biotechnology and Aquaculture ; Hellenic Centre for Marine Research ; 71003 ; Heraklion ; Greece
  33. Department of Animal and Food Sciences ; University of Delaware ; Newark ; DE ; 19716 ; USA
  34. Animal Production and Protection ; United States Department of Agriculture ; Agricultural Research Service Aquaculture ; Beltsville ; MD ; 20705 ; USA
  35. CSIRO Agriculture ; Commonwealth Scientific and Industrial Research Organisation ; St Lucia ; 4067 ; Australia
  36. Green Technology ; Natural Resources Institute Finland ; 31600 ; Jokioinen ; Finland
  37. Animal Disease Research Unit ; United States Department of Agriculture ; Agricultural Research Service ; Pullman ; WA ; 99164-6630 ; USA
  38. Department of Veterinary Microbiology and Pathology ; Washington State University ; Pullman ; WA ; 99164-7040 ; USA
  39. Key Laboratory of Agricultural Animal Genetics ; Breeding and Reproduction of Ministry of Education of China ; Huazhong Agricultural University ; Wuhan ; Hubei ; 430070 ; People鈥檚 Republic of China
  40. Department of Animal Science ; University of California ; Davis ; CA ; 95616 ; USA
  
• 刊名：Genome Biology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：353 KB
• 参考文献：An integrated encyclopedia of DNA elements in the human genome. Nature 489: pp. 57-74 247" target="_blank" title="It opens in new window">CrossRef
  1. Andersson, L (2013) Molecular consequences of animal breeding. Curr Opin Genet Dev 23: pp. 295-301 2013.02.014" target="_blank" title="It opens in new window">CrossRef
  2. Freking, BA, Murphy, SK, Wylie, AA, Rhodes, SJ, Keele, JW, Leymaster, KA (2002) Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. Genome Res 12: pp. 1496-1506 2" target="_blank" title="It opens in new window">CrossRef
  3. Clop, A, Marcq, F, Takeda, H, Pirottin, D, Tordoir, X, Bib茅, B (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38: pp. 813-818 CrossRef
  4. Laere, AS, Nguyen, M, Braunschweig, M, Nezer, C, Collette, C, Moreau, L (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425: pp. 832-836 2064" target="_blank" title="It opens in new window">CrossRef
  5. Andersson, LS, Larhammar, M, Memic, F, Wootz, H, Schwochow, D, Rubin, CJ (2012) Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488: pp. 642-646 CrossRef
  6. Schaub, MA, Boyle, AP, Kundaje, A, Batzoglou, S, Snyder, M (2012) Linking disease associations with regulatory information in the human genome. Genome Res 22: pp. 1748-1759 27.111" target="_blank" title="It opens in new window">CrossRef
  Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: pp. 695-716 CrossRef
  7. Groenen, MA, Archibald, AL, Uenishi, H, Tuggle, CK, Takeuchi, Y, Rothschild, MF (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491: pp. 393-398 22" target="_blank" title="It opens in new window">CrossRef
  8. Elsik, CG, Tellam, RL, Worley, KC, Gibbs, RA, Muzny, DM, Weinstock, GM (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: pp. 522-528 26/science.1169588" target="_blank" title="It opens in new window">CrossRef
  9. Jiang, Y, Xie, M, Chen, W, Talbot, R, Maddox, JF, Faraut, T (2014) The sheep genome illuminates biology of the rumen and lipid metabolism. Science 344: pp. 1168-1173 26/science.1252806" target="_blank" title="It opens in new window">CrossRef
  10. Brawand, D, Wagner, CE, Li, YI, Malinsky, M, Keller, I, Fan, S (2014) The genomic substrate for adaptive radiation in African cichlid fish. Nature 513: pp. 375-381 26" target="_blank" title="It opens in new window">CrossRef
  11. Rubin, CJ, Zody, MC, Eriksson, J, Meadows, JR, Sherwood, E, Webster, MT (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: pp. 587-591 2" target="_blank" title="It opens in new window">CrossRef
  12. Carneiro, M, Rubin, CJ, Palma, F, Albert, FW, Alfoldi, J, Barrio, AM (2014) Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345: pp. 1074-1079 26/science.1253714" target="_blank" title="It opens in new window">CrossRef
  13. Freedman, AH, Gronau, I, Schweizer, RM, Ortega-Del Vecchyo, D, Han, E (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genet 10: pp. e1004016 CrossRef
  14. Larkin, DM, Daetwyler, HD, Hernandez, AG, Wright, CL, Hetrick, LA, Boucek, L (2012) Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle. Proc Natl Acad Sci U S A 109: pp. 7693-7698 CrossRef
  15. Rubin, CJ, Megens, HJ, Martinez Barrio, A, Maqbool, K, Sayyab, S, Schwochow, D (2012) Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A 109: pp. 19529-19536 217149109" target="_blank" title="It opens in new window">CrossRef
  16. Schubert, M, J贸nsson, H, Chang, D, Sarkissian, C, Ermini, L, Ginolhac, A (2014) Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proc Natl Acad Sci U S A 111: pp. E5661-E5669 CrossRef
  17. Guilbault, C, Saeed, Z, Downey, GP, Radzioch, D (2007) Cystic fibrosis mouse models. Am J Respir Cell Mol Biol 36: pp. 1-7 2006-0184TR" target="_blank" title="It opens in new window">CrossRef
  18. Devoy, A, Bunton-Stasyshyn, RK, Tybulewicz, VL, Smith, AJ, Fisher, EM (2012) Genomically humanized mice: technologies and promises. Nat Rev Genet 13: pp. 14-20 CrossRef
  19. Walters, EM, Wolf, E, Whyte, JJ, Mao, J, Renner, S, Nagashima, H (2012) Completion of the swine genome will simplify the production of swine as a large animal biomedical model. BMC Med Genomics 5: pp. 55 CrossRef
  20. Hill, WG (2014) Applications of population genetics to animal breeding, from Wright, Fisher and Lush to genomic prediction. Genetics 196: pp. 1-16 2.147850" target="_blank" title="It opens in new window">CrossRef
  21. Meuwissen, TH, Hayes, BJ, Goddard, ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: pp. 1819-1829
  22. Meuwissen, T, Goddard, M (2010) Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185: pp. 623-631 CrossRef
  23. Daetwyler, HD, Capitan, A, Pausch, H, Stothard, P, Binsbergen, R, Brondum, RF (2014) Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet 46: pp. 858-865 CrossRef
  24. MacLeod, IM, Hayes, BJ, Goddard, ME (2014) The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics 198: pp. 1671-1684 CrossRef
  25. Koufariotis, L, Chen, YP, Bolormaa, S, Hayes, BJ (2014) Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle. BMC Genomics 15: pp. 436 2164-15-436" target="_blank" title="It opens in new window">CrossRef
  26. Shen, Y, Yue, F, McCleary, DF, Ye, Z, Edsall, L, Kuan, S (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488: pp. 116-120 243" target="_blank" title="It opens in new window">CrossRef
  27. Yue, F, Cheng, Y, Breschi, A, Vierstra, J, Wu, W, Ryba, T (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515: pp. 355-364 2" target="_blank" title="It opens in new window">CrossRef
  28. Roy, S, Ernst, J, Kharchenko, PV, Kheradpour, P, Negre, N, Eaton, ML (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: pp. 1787-1797 26/science.1198374" target="_blank" title="It opens in new window">CrossRef
  29. Gerstein, MB, Lu, ZJ, Nostrand, EL, Cheng, C, Arshinoff, BI, Liu, T (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330: pp. 1775-1787 26/science.1196914" target="_blank" title="It opens in new window">CrossRef
  30. Sivasubbu, S, Sachidanandan, C, Scaria, V (2013) Time for the zebrafish ENCODE. J Genet 92: pp. 695-701 2041-013-0313-4" target="_blank" title="It opens in new window">CrossRef
  31. Barbosa-Morais, NL, Irimia, M, Pan, Q, Xiong, HY, Gueroussov, S, Lee, LJ (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338: pp. 1587-1593 26/science.1230612" target="_blank" title="It opens in new window">CrossRef
  32. Schmidt, D, Wilson, MD, Ballester, B, Schwalie, PC, Brown, GD, Marshall, A (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: pp. 1036-1040 26/science.1186176" target="_blank" title="It opens in new window">CrossRef
  33. Tagu, D, Colbourne, JK, N猫gre, N (2014) Genomic data integration for ecological and evolutionary traits in non-model organisms. BMC Genomics 15: pp. 490 2164-15-490" target="_blank" title="It opens in new window">CrossRef
  34. Bae, JB (2013) Perspectives of international human epigenome consortium. Genomics Inform 11: pp. 7-14 2013.11.1.7" target="_blank" title="It opens in new window">CrossRef
  35. Birney, E, Hudson, TJ, Green, ED, Gunter, C, Eddy, S, Rogers, J (2009) Prepublication data sharing. Nature 461: pp. 168-170 CrossRef
  36. The FAANG Consortium. http://www.faang.org
  37. Stamatoyannopoulos, JA (2012) What does our genome encode?. Genome Res 22: pp. 1602-1611 2" target="_blank" title="It opens in new window">CrossRef
  38. Landt, SG, Marinov, GK, Kundaje, A, Kheradpour, P, Pauli, F, Batzoglou, S (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22: pp. 1813-1831 CrossRef
  39. Birney, E (2012) The making of ENCODE: lessons for big-data projects. Nature 489: pp. 49-51 CrossRef
  40. Eddy, SR (2013) The ENCODE project: missteps overshadowing a success. Curr Biol 23: pp. R259-R261 2013.03.023" target="_blank" title="It opens in new window">CrossRef
  41. Parkhomchuk, D, Borodina, T, Amstislavskiy, V, Banaru, M, Hallen, L, Krobitsch, S (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: pp. e123 CrossRef
  42. Derrien, T, Johnson, R, Bussotti, G, Tanzer, A, Djebali, S, Tilgner, H (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22: pp. 1775-1789 2159.111" target="_blank" title="It opens in new window">CrossRef
  43. Harrow, J, Frankish, A, Gonzalez, JM, Tapanari, E, Diekhans, M, Kokocinski, F (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22: pp. 1760-1774 CrossRef
  44. Mudge, JM, Frankish, A, Harrow, J (2013) Functional transcriptomics in the post-ENCODE era. Genome Res 23: pp. 1961-1973 CrossRef
  45. Thurman, RE, Rynes, E, Humbert, R, Vierstra, J, Maurano, MT, Haugen, E (2012) The accessible chromatin landscape of the human genome. Nature 489: pp. 75-82 232" target="_blank" title="It opens in new window">CrossRef
  46. Buenrostro, JD, Giresi, PG, Zaba, LC, Chang, HY, Greenleaf, WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: pp. 1213-1218 2688" target="_blank" title="It opens in new window">CrossRef
  47. Buenrostro, JD, Wu, B, Chang, HY, Greenleaf, WJ (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109: pp. 21.29.1-21.29.9 2/0471142727.mb2129s109" target="_blank" title="It opens in new window">CrossRef
  48. Ong, CT, Corces, VG (2014) CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15: pp. 234-246 CrossRef
  49. Ho, JW, Jung, YL, Liu, T, Alver, BH, Lee, S, Ikegami, K (2014) Comparative analysis of metazoan chromatin organization. Nature 512: pp. 449-452 CrossRef
  50. Meissner, A, Gnirke, A, Bell, GW, Ramsahoye, B, Lander, ES, Jaenisch, R (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33: pp. 5868-5877 CrossRef
  51. van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, / et al. Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp 2010;39:pii:1869.
  52. Rao, SS, Huntley, MH, Durand, NC, Stamenova, EK, Bochkov, ID, Robinson, JT (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159: pp. 1665-1680 2014.11.021" target="_blank" title="It opens in new window">CrossRef
  
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
• 出版者：BioMed Central
• ISSN：1465-6906

文摘

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.