Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis

G3: Genes, Genomes, Genetics

Volumn 3, Issue 2, 2013, Pages 359-367

  Dlugosch, Katrina M ^a,b   Lai, Zhao ^c   Bonin, Aurélie ^c   Hierro, Josè ^d   Rieseberg, Loren H ^a,c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b University of Arizona   (United States)

^c INDIANA UNIVERSITY   (United States)

^d UNIVERSIDAD NACIONAL DE LA PAMPA   (Argentina)

Author keywords

454 GS FLX; Allele clustering; Invasive species; Normalized ESTs; Titanium; Yellow starthistle

Indexed keywords

TRANSCRIPTOME;

ALLELE; ARABIDOPSIS THALIANA; ARTICLE; CENTAUREA; CENTAUREA SOLSTITIALIS; DNA SYNTHESIS; GENE IDENTIFICATION; GENE NUMBER; GENE ONTOLOGY; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; GENOMICS; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT SEED; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; TOMATO; TRANSCRIPTOMICS; 454 GS FLX TITANIUM; ALLELE CLUSTERING; CLUSTER ANALYSIS; COMPUTER PROGRAM; FACTUAL DATABASE; GENE LIBRARY; GENE LOCUS; GENETICS; HIGH THROUGHPUT SEQUENCING; INTRODUCED SPECIES; INVASIVE SPECIES; METAGENOMICS; NORMALIZED ESTS; PLANT GENOME; YELLOW STARTHISTLE;

CENTAUREA; CENTAUREA SOLSTITIALIS;

454 GS FLX TITANIUM; ALLELE CLUSTERING; INVASIVE SPECIES; NORMALIZED ESTS; YELLOW STARTHISTLE;

ALLELES; CENTAUREA; CLUSTER ANALYSIS; DATABASES, FACTUAL; GENE LIBRARY; GENETIC LOCI; GENOME, PLANT; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTRODUCED SPECIES; METAGENOMICS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; TRANSCRIPTOME;

EID: 84883182719     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.003871     Document Type: Article

References (73)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Angeloni, F., C. A. M. Wagemaker, M. S. M. Jetten, H. J. M. Op den Camp, E. M. Jassen-Megens, et al. 2011 De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using nextgeneration sequencing techniques. Mol. Ecol. Res. 11: 662-674.
3. Avise, J. C., 2004 Molecular Markers, Natural History, and Evolution. Sinauer Associates, Sunderland, MA.
4. Barbazuk,W. B., S. J. Emrich, H. D. Chen, L. Li, and P. S. Schnable, 2007 SNP discovery via 454 transcriptome sequencing. Plant J. 51: 910-918.
5. Barbazuk, W. B., Y. Fu, and K. M. McGinnis, 2008 Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res. 18: 1381-1392.
6. Barker, M. S., N. C. Kane, M. Matvienko, A. Kozik, W. Michelmore, et al. 2008 Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol. Biol. Evol. 25: 2445-2455.
7. Barker, M. S., K. M. Dlugosch, L. Dinh, R. S. Challa, N. C. Kane, et al. 2010 EvoPipes.net: bioinformatic tools for ecological and evolutionary genomics. Evol. Bioinf. 6: 143-149.
8. Barker, M. S., G. J. Baute, and S.-L. Liu, 2012 Duplication and turnover in plant genomes, pp. 155-169 in Plant Genome Diversity, edited by J. F. Wendel. Springer, Vienna.
9. Barreto, F. S., G. W. Moy, and R. S. Burton, 2011 Interpopulation patterns of divergence and selection across the transcriptome of the copepod Tigriopus californicus. Mol. Ecol. 20: 560-572.
10. Beldade, P., S. Rudd, J. D. Gruber, and A. D. Long, 2006 A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. BMC Genomics 7: 130.
11. Bentley, D. R., 2006 Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16: 545-552.
12. Bergelson, J., M. Kreitman, E. A. Stahl, and D. Tian, 2001 Evolutionary dynamics of plant R-genes. Science 292: 2281-2285.
13. Bouck, A., and T. Vision, 2007 The molecular ecologist's guide to expressed sequence tags. Mol. Ecol. 16: 907-924.
14. Brancheva, S., and J. Greilhuber, 2006 Genome size in Bulgarian Centaurea s.l. (Asteraceae). Plant Syst. Evol. 257: 95-117.
15. Charlesworth, B., 2010 Molecular population genomics: a short history. Genet. Res. 92: 397-411.
16. Chevreux, B., T. Pfisterer, B. Drescher, A. J. Driesel, W. E. G. Muller, et al. 2004 Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14: 1147-1159.
17. Christodoulou, D. C., J. M. Gorham, D. S. Herman, and J. G. Seidman, 2011 Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr. Prot. Mol. Biol. 94: 4.12.1-4.12.11.
18. Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen, et al. 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499-510.
19. Dempewolf, H., N. C. Kane, K. L. Ostevik, M. Geleta,M. S. Barker, et al. 2010 Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol. Ecol. Res. 10: 1048-1058.
20. Demuth, J. P., T. De Bie, J. E. Stajich, N. Cristianini, and M. W. Hahn, 2006 The evolution of mammalian gene families. PLoS ONE 1: e85.
21. Dlugosch, K. M., and A. Bonin, 2012 Allele identification in assembled genomic sequence datasets, pp. 197-211 in Methods in Molecular Biology Series: Data Production and Analysis in Population Genomics, edited by A. Bonin, and F. Pompanon. Springer, New York.
22. Dlugosch, K. M., and I. M. Parker, 2008 Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions. Mol. Ecol. 17: 431-449.
23. Drosophila 12 Genomes Consortium, 2007 Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
24. Duarte, J. M., P. K. Wall, P. P. Edger, L. L. Landherr, H. Ma, et al. 2010 Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evol. Biol. 10: 61.
25. Durbin, R. M., D. Altshuler, G. R. Abecasis, D. R. Bentley, A. Chakravarti, et al. 2010 A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
26. Elmer, K. R., S. Fan, H. M. Gunter, J. C. Jones, S. Boekhoff, et al. 2010 Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol. Ecol. 19: 197-211.
27. Emerson, K. J., C. R. Merz, J. M. Catchen, P. A. Hohenlohe, W. A. Cresko, et al. 2010 Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. USA 107: 16196-16200.
28. Falush, D., M. Stephens, and J. K. Pritchard, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
29. Gerlach, J., 1997 How the west was lost: reconstructing the invasion dynamics of yellow starthistle and other plant invaders of western rangelands and natural areas. California Exotic Pest Plant Council Symp. Proc. 3: 67-72.
30. Hahn, M. W., T. De Bie, J. E. Stajich, C. Nguyen, and N. Cristianini, 2005 Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 15: 1153-1160.
31. Hahn, M. W., M. V. Han, and S.-G. Han, 2007 Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3: e197.
32. Hamrick, J. L., and M. J. Godt, 1989 Allozyme diversity in plant species, pp. 43-63 in Plant Population Genetics, Breeding and Germplasm Resources, edited by A. H. D.,M. T. Brown, A. L. Clegg, Kahler, and B. S.Weir. Sinauer, Sunderland.
33. Hancock, A. M., B. Brachi, N. Faure, M. W. Horton, L. B. Jarymowycz, et al. 2011 Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
34. Heiser, C. B., and T. W. Whitaker, 1948 Chromosome number, polyploidy, and growth habit in California weeds. Am. J. Bot. 35: 179-186.
35. Huang, X., and A. Madan, 1999 CAP3: a DNA sequence assembly program. Genome Res. 9: 868-877.
36. Kozik, A., M. Matvienko, I. Kozik, H. Van Leeuwen, A. Van Deynze, et al. 2008 Eukaryotic ultra conserved orthologs and estimation of gene capture in EST libraries. Plant and Animal Genome Conference XVI: P6.
37. Lai, Z., N. C. Kane, A. Kozik, K. Hodgins, K. M. Dlugosch, et al. 2012 Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression. Am. J. Bot. 99: 209-218.
38. Lassmann, T., Y. Hayashizaki, and C. O. Daub, 2009 TagDust-a program to eliminate artifacts from next generation sequencing data. Bioinfomatics 25: 2839-2840.
39. Lawlor, D. A., F. E. Ward, P. D. Ennis, A. P. Jackson, and P. Parham, 1988 HLA-A and B polymorphisms predate the divergence of humans and chimpanzees. Nature 335: 268-271.
40. Lewontin, R. C., and J. L. Hubby, 1966 A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595-609.
41. Li, H., J. Ruan, and R. Durbin, 2008 Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858.
42. Li, W. H., and L. A. Sadler, 1991 Low nucleotide diversity in man. Genetics 129: 513-523.
43. Lynch, M., and J. S. Conery, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
44. Maddox, D. M., A. Mayfield, and N. H. Poritz, 1985 Distribution of yellow starthistle (Centaurea solstitialis) and Russian knapweed (Centaurea repens). Weed Sci. 33: 315-327.
45. Margulies,M., M. Egholm,W. E. Altman, S. Attiya, J. S. Bader, et al. 2005 Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
46. McCarthy, M. I., G. R. Abecasis, L. R. Cardon, D. B. Goldstein, J. Little, et al. 2008 Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet. 9: 356-369.
47. Meyer, E., G. V. Aglyamova, S. Wang, J. Buchanan-Carter, D. Abrego, et al. 2009 Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 10: 219.
48. Morin, P. A., G. Luikart, and R. K.Wayne SNP Wokshop Group, 2004 SNPs in ecology, evolution and conservation. Trends Ecol. Evol. 19: 208-216.
49. Moriyama, E. N., and J. R. Powell, 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
50. Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song, 2011 Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443-451.
51. Ning, Z., A. J. Cox, and J. C. Mullikin, 2001 SSAHA: a fast search method for large DNA databases. Genome Res. 11: 1725-1729.
52. Ossowski, S., K. Schneeberger, R. M. Clark, C. Lanz, N. Warthmann, et al. 2008 Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 18: 2024-2033.
53. Ozturk, M., E. Martin, M. Dinc, A. Duran, A. Ozdemir, et al. 2009 A cytogenetical study on some plant taxa in Nizip region (Aksaray, Turkey). Turk. J. Biol. 33: 35-44.
54. Prentis, P. J., J. R. U. Wilson, E. E.Dormontt,D.M. Richardson, and A. J. Lowe, 2008 Adaptive evolution in invasive species. Trends Plant Sci. 13: 288-294.
55. Pritchard, J. K., M. Stephens, and P. Donnell, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
56. R Development Core Team, 2010 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
57. Renaut, S., A. W. Nolte, and L. Bernatchez, 2010 Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Mol. Ecol. 19: 115-131.
58. Rosenberg, N. A., 2004 Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes 4: 137-138.
59. Sebat, J., B. Lakshmi, J. Troge, J. Alexander, J. Young, et al. 2004 Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
60. Seeb, J. E., C. E. Pascal, E. D. Grau, L. W. Seeb, W. D. Templin, et al. 2011 Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol. Ecol. Res. 11: 335-348.
61. Sun, M., 1997 Population genetic structure of yellow starthistle (Centaurea solstitialis), a colonizing weed in the western United States. Can. J. Bot. 75: 1470-1478.
62. Sun, M., and K. Ritland, 1998 Mating system of yellow starthistle (Centaurea solstitialis), a successful colonizer in North America. Heredity 80: 225-232.
63. The Tomato Genome Consortium, 2012 The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
64. Ueno, S.,G. Le Provost, V. Lèger, C. Klopp, C.Noirot, et al. 2010 Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11: 650.
65. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, et al. 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.
66. Wakeley, J., 2008 Coalescent Theory: An introduction. Roberts & Company Publishers, Greenwood Village. CO.
67. Wheat, C. W., 2010 Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138: 433-451.
68. Widmer, T., F. Guermache, M. Dolgovskaia, and S. Reznick, 2007 Enhanced growth and seed properties in introduced vs. native populations of yellow starthistle (Centaurea solstitialis). Weed Sci. 55: 465-473.
69. Wilson, L. M., C. Jette, J. Connett, and J. McCaffrey, 2003 Biology and Biological Control of Starthistle. USDA Forest Service / University of Nebraska Lincoln Faculty Publications, Lincoln, NB.
70. Zakas, C., N. Schult, D. McHugh, K. L. Jones, and J. P. Wares, 2012 Transcriptome analysis and SNP development can resolve population differentiation of Streblospio benedicti, a developmentally dimorphic marine annelid. PLoS ONE 7: e3161.
71. Zayed, A., and C. W. Whitfield, 2008 A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. Proc. Natl. Acad. Sci. USA 105: 3421-3426.
72. Zheng, Y., L. Zhao, J. Gao, and Z. Fei, 2011 iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinf. 12: 453.
73. Zhulidov, P. A., E. A. Bogdanova, A. S. Shcheglov, L. L. Vagner, and G. L. Khaspekov, 2004 Simple cDNA normalization using kamchatka crab duplex specific nuclease. Nucleic Acids Res. 32: e37.