Sequencing, assembling, and correcting draft genomes using recombinant populations

G3: Genes, Genomes, Genetics

Volumn 4, Issue 4, 2014, Pages 669-679

  Hahn, Matthew W ^a,b   Zhang, Simo V ^b   Moyle, Leonie C ^a  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Assembly; Duplication; Genetics; Genome; Next Generation sequencing

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; CAENORHABDITIS ELEGANS; FEMALE; GENE DUPLICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC LINKAGE; GENETIC PARAMETERS; GENOME ANALYSIS; GENOME ASSEMBLY; GENOMICS; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; NONHUMAN; RECOMBINANT POPULATION GENOME CONSTRUCTION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84898855509     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.010264     Document Type: Article

References (55)

1. Adams, M. D., S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne et al., 2000 The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Alkan, C., S. Sajjadian, and E. E. Eichler, 2011 Limitations of next-generation genome sequence assembly. Nat. Methods 8: 61-65.
3. Amores, A., J. Catchen, A. Ferrara, Q. Fontenot, and J. H. Postlethwait, 2011 Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 188: 799-808.
4. Bailey, J. A., A. M. Yavor, H. F. Massa, B. J. Trask, and E. E. Eichler, 2001 Segmental duplications: organization and impact within the current Human Genome Project assembly. Genome Res. 11: 1005-1017.
5. Bailey, J. A., Z. P. Gu, R. A. Clark, K. Reinert, R. V. Samonte et al., 2002 Recent segmental duplications in the human genome. Science 297: 1003-1007.
6. Baird, N. A., P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver et al., 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376.
7. Bansal, V., A. L. Halpern, N. Axelrod, and V. Bafna, 2008 An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res. 18: 1336-1346.
8. Barrière, A., S.-P. Yang, E. Pekarek, C. G. Thomas, E. S. Haag et al., 2009 Detecting heterozygosity in shotgun genome assemblies: lessons from obligately outcrossing nematodes. Genome Res. 19: 470-480.
9. Browning, S. R., and B. L. Browning, 2007 Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81: 1084-1097.
10. Casola, C., C. L. Ganote, and M. W. Hahn, 2010 Nonallelic gene conversion in the genus Drosophila. Genetics 185: 95-103.
11. Chagné, D., G. Brown, C. Lalanne, D. Madur, D. Pot et al., 2003 Comparative genome and QTL mapping between maritime and loblolly pines. Mol. Breed. 12: 185-195.
12. Cheung, J., X. Estivill, R. Khaja, J. MacDonald, K. Lau et al., 2003 Genomewide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4: R25.
13. Colbourne, J. K., M. E. Pfrender, D. Gilbert, W. K. Thomas, A. Tucker et al., 2011 The ecoresponsive genome of Daphnia pulex. Science 331: 555-561.
14. C. elegans Sequencing Consortium, 1998 Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
15. Dehal, P., Y. Satou, R. K. Campbell, J. Chapman, B. Degnan et al., 2002 The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298: 2157-2167.
16. Denoeud, F., S. Henriet, S. Mungpakdee, J. M. Aury, C. Da Silva et al., 2010 Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330: 1381-1385.
17. Genovese, G., R. E. Handsaker, H. Li, N. Altemose, A. M. Lindgren et al., 2013 Using population admixture to help complete maps of the human genome. Nat. Genet. 45: 406-414.
18. Gnerre, S., I. MacCallum, D. Przybylski, F. J. Ribeiro, J. N. Burton et al., 2011 High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. USA 108: 1513-1518.
19. Grattapaglia, D., and R. Sederoff, 1994 Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137: 1121-1137.
20. Hall, M. C., and J. H. Willis, 2005 Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. Genetics 170: 375-386.
21. Han, M. V., J. P. Demuth, C. L. McGrath, C. Casola, and M. W. Hahn, 2009 Adaptive evolution of young duplicated genes in mammals. Genome Res. 19: 859-867.
22. Haridas, S., C. Breuill, J. Bohlmann, and T. Hsiang, 2011 A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes. J. Microbiol. Methods 86: 368-375.
23. Harris, R. S., 2007 Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University.
24. Holt, R. A., G. M. Subramanian, A. Halpern, G. G. Sutton, R. Charlab et al., 2002 The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
25. Hu, X., J. Yuan, Y. Shi, J. Lu, B. Liu et al., 2012 pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 28: 1533-1535.
26. Huang, X., Q. Feng, Q. Qian, Q. Zhao, L. Wang et al., 2009 Highthroughput genotyping by whole-genome resequencing. Genome Res. 19: 1068-1076.
27. Hyten, D. L., S. B. Cannon, Q. Song, N. Weeks, E. W. Fickus et al., 2010 High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.
28. Kelley, D. R., and S. L. Salzberg, 2010 Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol. 11: R28.
29. Kim, J. H., M. S. Waterman, and L. M. Li, 2007 Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 17: 1101-1110.
30. Kitzman, J. O., A. P. MacKenzie, A. Adey, J. B. Hiatt, R. P. Patwardhan et al., 2011 Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat. Biotechnol. 29: 59-63.
31. Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al., 2001 Initial sequencing and analysis of the human genome. Nature 409: 860-921.
32. Langley, C. H., K. Stevens, C. Cardeno, Y. C. G. Lee, D. R. Schrider et al., 2012 Genomic variation in natural populations of Drosophila melanogaster. Genetics 192: 533-598.
33. Lewin, H. A., D. M. Larkin, J. Pontius, and S. J. O'Brien, 2009 Every genome sequence needs a good map. Genome Res. 19: 1925-1928.
34. Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
35. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
36. Lin, Y., J. Li, H. Shen, L. Zhang, C. J. Papasian et al., 2011 Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 27: 2031-2037.
37. Mackay, T. F. C., S. Richards, E. A. Stone, A. Barbadilla, J. F. Ayroles et al., 2012 The Drosophila melanogaster Genetic Reference Panel. Nature 482: 173-178.
38. Matsubara, K., K. Ebana, T. Mizubayashi, S. Itoh, T. Ando et al., 2011 Relationship between transmission ratio distortion and genetic divergence in intraspecific rice crosses. Mol. Genet. Genomics 286: 307-319.
39. McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., 2010 The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20: 1297-1303.
40. Mortazavi, A., E. M. Schwarz, B. Williams, L. Schaeffer, I. Antoshechkin et al., 2010 Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res. 20: 1740-1747.
41. Moyle, L. C., and E. B. Graham, 2006 Genome-wide associations between hybrid sterility QTL and marker transmission ratio distortion. Mol. Biol. Evol. 23: 973-980.
42. Myburg, A. A., C. Vogl, A. R. Griffin, R. R. Sederoff, and R. W. Whetten, 2004 Genetics of postzygotic isolation in eucalyptus: whole-genome analysis of barriers to introgression in a wide interspecific cross of Eucalyptus grandis and E. globulus. Genetics 166: 1405-1418.
43. Payseur, B. A., and H. E. Hoekstra, 2005 Signatures of reproductive isolation in patterns of single nucleotide diversity across inbred strains of mice. Genetics 171: 1905-1916.
44. Ross, J. A., D. C. Koboldt, J. E. Staisch, H. M. Chamberlin, B. P. Gupta et al., 2011 Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS Genet. 7: e1002174.
45. Sackton, T. B., R. J. Kulathinal, C. M. Bergman, A. R. Quinlan, E. B. Dopman et al., 2009 Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol. Evol. 1: 449-465.
46. Schatz, M. C., A. L. Delcher, and S. L. Salzberg, 2010 Assembly of large genomes using second-generation sequencing. Genome Res. 20: 1165-1173.
47. Solignac, M., D. Vautrin, E. Baudry, F. Mougel, A. Loiseau et al., 2004 A microsatellite-based linkage map of the honeybee, Apis mellifera L. Genetics 167: 253-262.
48. Tautz, D., H. Ellegren, and D. Weigel, 2011 Next generation molecular ecology. Mol. Ecol. 19: 1-3.
49. Tulsieram, L. K., J. C. Glaubitz, G. Kiss, and J. E. Carlson, 1992 Single tree genetic linkage mapping in conifers using haploid DNA from megagametophytes. Nat. Biotechnol. 10: 686-690.
50. Wicks, S. R., R. T. Yeh, W. R. Gish, R. H. Waterston, and R. H. A. Plasterk, 2001 Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28: 160-164.
51. Wu, Y., P. R. Bhat, T. J. Close, and S. Lonardi, 2008 Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet. 4: e1000212.
52. Xie, W., Q. Feng, H. Yu, X. Huang, Q. Zhao et al., 2010 Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA 107: 10578-10583.
53. Ye, L., L. Hillier, P. Minx, N. Thane, D. P. Locke et al., 2011 A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 12: R31.
54. Zamir, D., and Y. Tadmor, 1986 Unequal segregation of nuclear genes in plants. Bot. Gaz. 147: 355-358.
55. Zhou, S., F. Wei, J. Nguyen, M. Bechner, K. Potamousis et al., 2009 A single molecule scaffold for the maize genome. PLoS Genet. 5: e1000711.