Developing maps of fitness consequences for plant genomes

Current Opinion in Plant Biology

Volumn 30, Issue , 2016, Pages 101-107

  Joly Lopez, Zoé ^a   Flowers, Jonathan M ^a,b   Purugganan, Michael D ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; GENOMICS; PHYSIOLOGY; PLANT GENOME; PROCEDURES;

GENOME, PLANT; GENOMICS; POLYMORPHISM, GENETIC; SELECTION, GENETIC;

EID: 84959265979     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2016.02.008     Document Type: Review

References (67)

1. Bajaj D., Das S., Badoni S., Kumar V., Singh M., Bansal K.C., Tyagi A.K., Parida S.K. Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea. Sci Rep 2015, 5:12468.
2. Unterseer S., Bauer E., Haberer G., Seidel M., Knaak C., Ouzunova M., Meitinger T., Strom T.M., Fries R., Pausch H., et al. A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array. BMC Genomics 2014, 15:823.
3. Alexandrov N., Tai S., Wang W., Mansueto L., Palis K., Fuentes R.R., Ulat V.J., Chebotarov D., Zhang G., Li Z., et al. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res 2015, 43:D1023-D1027.
4. Hazzouri K.M., Flowers J.M., Visser H.J., Khierallah H.S.M., Rosas U., Pham G.M., Meyer R.S., Johansen C.K., Patrick Z.F., Masmoudi K., et al. Whole genome re-sequencing of date palms yield insights into diversification of a fruit tree crop. Nat Commun 2015, 6:8824.
5. Flowers J.M., Hazzouri K.M., Pham G.M., Rosas U., Bahmani T., Khraiwesh B., Nelson D.R., Jijakli K., Abdrabu R., Harris E.H., et al. Whole-genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. Plant Cell 2015, 27:2353-2369.
6. Li J.Y., Wang J., Zeigler R.S. The 3000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 2014, 3:8.
7. Kimura M. The Neutral Theory of Molecular Evolution 1984, Cambridge University Press.
8. Eyre-Walker A., Keightley P.D. The distribution of fitness effects of new mutations. Nat Rev Genet 2007, 8:610-618.
9. Graur D., Zheng Y., Price N., Azevedo R.B., Zufall R.A., Elhaik E. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013, 5:578-590.
10. Albert F.W., Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015, 16:197-212.
11. Huang X., Han B. Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol 2014, 65:531-551.
12. Pollard K.S., Hubisz M.J., Rosenbloom K.R., Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010, 20:110-121.
13. Siepel A., Bejerano G., Pedersen J.S., Hinrichs A.S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L.W., Richards S., et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005, 15:1034-1050.
14. Cooper G.M., Stone E.A., Asimenos G., Program N.C.S., Green E.D., Batzoglou S., Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15:901-913.
15. Goodstein D.M., Shu S., Howson R., Neupane R., Hayes R.D., Fazo J., Mitros T., Dirks W., Hellsten U., Putnam N., et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012, 40:D1178-D1186.
16. Haudry A., Platts A.E., Vello E., Hoen D.R., Leclercq M., Williamson R.J., Forczek E., Joly-Lopez Z., Steffen J.G., Hazzouri K.M., et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 2013, 45:891-898.
17. Lawrie D.S., Petrov D.A. Comparative population genomics: power and principles for the inference of functionality. Trends Genet 2014, 30:133-139.
18. Burgess D.G., Xu J., Freeling M. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. Curr Opin Plant Biol 2015, 27:141-147.
19. Henn B.M., Botigue L.R., Bustamante C.D., Clark A.G., Gravel S. Estimating the mutation load in human genomes. Nat Rev Genet 2015, 16:333-343.
20. Fay J.C., Wyckoff G.J., Wu C.I. Positive and negative selection on the human genome. Genetics 2001, 158:1227-1234.
21. Eyre-Walker A., Woolfit M., Phelps T. The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 2006, 173:891-900.
22. Mezmouk S., Ross-Ibarra J. The pattern and distribution of deleterious mutations in maize. G3 (Bethesda) 2014, 4:163-171.
23. Renaut S., Rieseberg L.H. The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops. Mol Biol Evol 2015, 32:2273-2283.
24. Gulko B., Hubisz M.J., Gronau I., Siepel A. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet 2015, 47:276-283.
25. Gronau I., Arbiza L., Mohammed J., Siepel A. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol 2013, 30:1159-1171.
26. McDonald J.H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 1991, 351:652-654.
27. Sawyer S.A., Hartl D.L. Population genetics of polymorphism and divergence. Genetics 1992, 132:1161-1176.
28. Smith N.G., Eyre-Walker A. Adaptive protein evolution in Drosophila. Nature 2002, 415:1022-1024.
29. Andolfatto P. Adaptive evolution of non-coding DNA in Drosophila. Nature 2005, 437:1149-1152.
30. Kircher M., Witten D.M., Jain P., O'Roak B.J., Cooper G.M., Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014, 46:310-315.
31. Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., Maglott D.R. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 2014, 42:D980-D985.
32. Seaver S.M., Gerdes S., Frelin O., Lerma-Ortiz C., Bradbury L.M., Zallot R., Hasnain G., Niehaus T.D., El Yacoubi B., Pasternak S., et al. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proc Natl Acad Sci U S A 2014, 111:9645-9650.
33. Kumar P., Henikoff S., Ng P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4:1073-1081.
34. Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. A method and server for predicting damaging missense mutations. Nat Methods 2010, 7:248-249.
35. Choi Y., Sims G.E., Murphy S., Miller J.R., Chan A.P. Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 2012, 7:e46688.
36. Adie E.A., Adams R.R., Evans K.L., Porteous D.J., Pickard B.S. SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 2006, 22:773-774.
37. Khurana J.K., Reeder J.E., Shrimpton A.E., Thakar J. GESPA: classifying nsSNPs to predict disease association. BMC Bioinformatics 2015, 16:228.
38. Shihab H.A., Gough J., Cooper D.N., Stenson P.D., Barker G.L., Edwards K.J., Day I.N., Gaunt T.R. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 2013, 34:57-65.
39. Deveci M., Catalyurek U.V., Toland A.E. mrSNP: software to detect SNP effects on microRNA binding. BMC Bioinformatics 2014, 15:73.
40. Sabarinathan R., Tafer H., Seemann S.E., Hofacker I.L., Stadler P.F., Gorodkin J. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat 2013, 34:546-556.
41. Mudvari P., Movassagh M., Kowsari K., Seyfi A., Kokkinaki M., Edwards N.J., Golestaneh N., Horvath A. SNPlice: variants that modulate Intron retention from RNA-sequencing data. Bioinformatics 2015, 31:1191-1198.
42. Katsonis P., Lichtarge O. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res 2014, 24:2050-2058.
43. Kovach M.J., Sweeney M.T., McCouch S.R. New insights into the history of rice domestication. Trends Genet 2007, 23:578-587.
44. Luo J., Liu H., Zhou T., Gu B., Huang X., Shangguan Y., Zhu J., Li Y., Zhao Y., Wang Y., et al. An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice. Plant Cell 2013, 25:3360-3376.
45. Hua L., Wang D.R., Tan L., Fu Y., Liu F., Xiao L., Zhu Z., Fu Q., Sun X., Gu P., et al. LABA1, a domestication gene associated with long, barbed awns in wild rice. Plant Cell 2015, 27:1875-1888.
46. Smith J.M., Haigh J. The hitch-hiking effect of a favourable gene. Genet Res 1974, 23:23-35.
47. Williamson R.J., Josephs E.B., Platts A.E., Hazzouri K.M., Haudry A., Blanchette M., Wright S.I. Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PLoS Genet 2014, 10:e1004622.
48. Wright S. Genetical structure of populations. Nature 1950, 166:247-249.
49. Holsinger K.E., Weir B.S. Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 2009, 10:639-650.
50. Wang M., Yu Y., Haberer G., Marri P.R., Fan C., Goicoechea J.L., Zuccolo A., Song X., Kudrna D., Ammiraju J.S., et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014, 46:982-988.
51. Cao J., Schneeberger K., Ossowski S., Gunther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 2011, 43:956-963.
52. Ciofani M., Madar A., Galan C., Sellars M., Mace K., Pauli F., Agarwal A., Huang W., Parkurst C.N., Muratet M., et al. A validated regulatory network for Th17 cell specification. Cell 2012, 151:289-303.
53. Miosge L.A., Field M.A., Sontani Y., Cho V., Johnson S., Palkova A., Balakishnan B., Liang R., Zhang Y., Lyon S., et al. Comparison of predicted and actual consequences of missense mutations. Proc Natl Acad Sci U S A 2015, 112:E5189-E5198.
54. Fowler D.M., Fields S. Deep mutational scanning: a new style of protein science. Nat Methods 2014, 11:801-807.
55. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
56. Feng Z., Zhang B., Ding W., Liu X., Yang D.L., Wei P., Cao F., Zhu S., Zhang F., Mao Y., et al. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 2013, 23:1229-1232.
57. Li J.F., Norville J.E., Aach J., McCormack M., Zhang D., Bush J., Church G.M., Sheen J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 2013, 31:688-691.
58. Jiang W., Zhou H., Bi H., Fromm M., Yang B., Weeks D.P. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 2013, 41:e188.
59. Wang Y., Cheng X., Shan Q., Zhang Y., Liu J., Gao C., Qiu J.L. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 2014, 32:947-951.
60. Liang Z., Zhang K., Chen K., Gao C. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genomics 2014, 41:63-68.
61. Bortesi L., Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 2015, 33:41-52.
62. Yang W., Guo Z., Huang C., Duan L., Chen G., Jiang N., Fang W., Feng H., Xie W., Lian X., et al. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun 2014, 5:5087.
63. Skinner M.E., Uzilov A.V., Stein L.D., Mungall C.J., Holmes I.H. JBrowse: a next-generation genome browser. Genome Res 2009, 19:1630-1638.
64. Lyons E., Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J 2008, 53:661-673.
65. Hartl D.L., Dykhuizen D.E., Dean A.M. Limits of adaptation: the evolution of selective neutrality. Genetics 1985, 111:655-674.
66. Rest J.S., Morales C.M., Waldron J.B., Opulente D.A., Fisher J., Moon S., Bullaughey K., Carey L.B., Dedousis D. Nonlinear fitness consequences of variation in expression level of a eukaryotic gene. Mol Biol Evol 2013, 30:448-456.
67. Katsonis P., Koire A., Wilson S.J., Hsu T.K., Lua R.C., Wilkins A.D., Lichtarge O. Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci 2014, 23:1650-1666.