Next-generation sequencing and systematics: What can a billion base pairs of DNA sequence data do for you?

Taxon

Volumn 60, Issue 6, 2011, Pages 1552-1566

  Harrison, Nicola ^a,b,c   Kidner, Catherine Anne ^a,b  

^a ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c EAST MALLING RESEARCH   (United Kingdom)

Author keywords

Next generation sequencing; Phylogenetics; Systematics; Taxonomy

Indexed keywords

ADAPTIVE RADIATION; GENE EXPRESSION; GENETIC STRUCTURE; HYBRIDIZATION; PHYLOGENETICS; PLANT COMMUNITY; POLYPLOIDY; TAXONOMY; TECHNOLOGICAL DEVELOPMENT;

EID: 84255195975     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.606002     Document Type: Review

References (172)

1. Abdelaziz, M., Lorite, J., Munoz-Pajares, A.J., Herrador, M.B., Perfectti, F. & Gomez, J.M. 2011. Using complementary techniques to distinguish cryptic species: A new Erysimum (Brassicaceae) species from North Africa. Amer. J. Bot. 98: 1049-1060.
2. Abrouk, M., Murat, F., Pont, C., Messing, J., Jackson, S., Faraut, T., Tannier, E., Plomion, C., Cooke, R., Feuillet, C. & Salse, J. 2010. Palaeogenomics of plants: Synteny-based modelling of extinct ancestors. Trends Pl. Sci. 15: 479-487.
3. Abzhanov, A., Extavour, C.G., Groover, A., Hodges, S.A., Hoekstra, H.E., Kramer, E.M. & Monteiro, A. 2008. Are we there yet? Tracking the development of new model systems. Trends Genet. 24: 353-360.
4. Altenhoff, A.M., Schneider, A., Gonnet, G.H. & Dessimoz, C. 2011. OMA 2011: Orthology inference among 1000 complete genomes. Nucl. Acids Res 39: D289-D294.
5. Anderson, J.T., Lee, C.R. & Mitchell-Olds, T. 2011. Life-history QTLs and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis. Evolution 65: 771-787.
6. Andolfatto, P., Davison, D., Erezyilmaz, D., Hu, T.T., Mast, J., Sunayama-Morita, T. & Stern, D.L. 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 21: 610-617.
7. Ansorge, W.J. 2009. Next-generation DNA sequencing techniques. Nat. Biotechnol. 25: 195-203.
8. Appleby, N., Edwards, D. & Batley, J. 2009. New technologies for ultra-high throughput genotyping in plants. Meth. Molec. Biol. 513: 19-39.
9. Atherton, R.A., McComish, B.J., Shepherd, L.D., Berry, L.A., Albert, N.W. & Lockhart, P.J. 2010. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform. Pl. Meth. 6: 22.
10. Baird, N.A., Etter, P.D., Atwood, T.S., Currey, M.C., Shiver, A.L., Lewis, Z.A., Selker, E.U., Cresko, W.A. & Johnson, E.A. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376. doi: 10.1371/journal.pone.0003376.
11. Banks, J.A., Nishiyama, T., Hasebe, M., Bowman, J.L., Gribskov, M., dePhamphilis, C. & al. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332: 960-963
12. Bao, S., Jiang, R., Kwan, W., Wang, B., Ma, X. & Song, Y.Q. 2011. Evaluation of next-generation sequencing software in mapping and assembly. J. Human Genet. 56: 406-414.
13. Barker, M.S., Dlugosch, K.M., Dinh, L., Challa, R.S., Kane, N.C., King, M.G. & Rieseberg, L.H. 2010. Evopipes.Net: Bioinformatic tools for ecological and evolutionary genomics. Evol. Bioinf. 6: 143-147.
14. Barrett, C.F. & Freudenstein, J.V. 2011. An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Molec. Ecol. 20: 2771-2786.
15. Becquet, C. & Przeworski, M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17: 1505-1519.
16. Bell, D., Long, D.G., Forrest, A.D., Hollingsworth, M.L., Blom, H.H. & Hollingsworth, P.M. 2011. DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species. Molec. Ecol. Resources, Early View. doi: 10.1111/j.1755-0998.2011.03053.x.
17. Blankenberg, D., Kuster, G. von, Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. & Taylor, J. 2010. Galaxy: A web-based genome analysis tool for experimentalists. Curr. Protoc. Molec. Biol. Chapter 19: 1-21.
18. Boussau, B. & Daubin, V. 2009. Genomes as documents of evolutionary history. Trends Ecol. Evol. 25: 224-232.
19. Bradshaw, H.D. & Schemske, D.W. 2003. Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature 426: 176-178.
20. Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X., Jovanovich, S.B., Krstic, P.S., Lindsay, S., Ling, X.S., Mastrangelo, C.H., Meller, A., Oliver, J.S., Pershin, Y.V., Ramsey, J.M., Riehn, R., Soni, G.V., Tabard-Cossa, V., Wanunu, M., Wiggin, M. & Schloss, J.A. 2008. The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26: 1146-1153.
21. Brautigam, A., Mullick, T., Schliesky, S. & Weber, A.P. 2011. Critical assessment of assembly strategies for non-model species mRNAseq data and application of next-generation sequencing to the comparison of C(3) and C(4) species. J. Exp. Bot. 62: 3093-3102.
22. Brower, A.V.Z., DeSalle, R., Vogler, A. 1996. Gene trees, species trees, and systematics: A cladistic perspective. Annual Rev. Ecol. Syst. 27: 423-450.
23. Bruni, I., De Mattia, F., Galimberti, A., Galasso, G., Banfi, E., Casiraghi, M. & Labra, M. 2010. Identification of poisonous plants by DNA barcoding approach. Int. J. Legal Med. 124: 595-603.
24. Buggs, R.J., Chamala, S., Wu, W., Gao, L., May, G.D., Schnable, P.S., Soltis, D.E., Soltis, P.S. & Barbazuk, W.B. 2010. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iplex massarray genotyping. Molec. Ecol. 19 (Suppl. 1): 132-146.
25. Burleigh, J.G., Hilu, K.W. & Soltis, D.E. 2009. Inferring phylogenies with incomplete data sets: A 5-gene, 567-taxon analysis of angiosperms. B. M. C. Evol. Biol. 9: 61. doi: 10.1186/1471-2148-9-61.
26. Cannon, S.B., Ilut, D., Farmer, A.D., Maki, S.L., May, G.D., Singer, S.R. & Doyle, J.J. 2010. Polyploidy did not predate the evolution of nodulation in all legumes. PLoS One 5: e11630. doi: 10.1371/ journal.pone.0011630.
27. CBOL Plant Working Group 2009. A DNA barcode for land plants. Proc. Natl. Acad. Sci. U.S.A. 106: 12794-12797.
28. Chan, E.Y. 2009. Next-generation sequencing methods: Impact of sequencing accuracy on SNP discovery. Meth. Molec. Biol. 578: 1-17.
29. Chase, M.W., Salamin, N., Wilkinson, M., Dunwell, J.M., Kesanakurthi, R.P., Haidar, N. & Savolainen, V. 2005. Land plants and DNA barcodes: Short-term and long-term goals. Philos. Trans., Ser. B 360: 1889-1895.
30. Chelaifa, H., Mahé, F. & Ainouche, M. 2010a. Transcriptome divergence between the hexaploid salt-marsh sister species Spartina maritima and Spartina alterniflora (Poaceae). Molec. Ecol. 19: 2050-2063.
31. Chelaifa, H., Monnier, A. & Ainouche, M. 2010b. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol. 186: 161-174.
32. Chutimanitsakun, Y., Nipper, R.W., Cuesta-Marcos, A., Cistue, L., Corey, A., Filichkina, T., Johnson, E.A. & Hayes, P.M. 2011. Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. B. M. C. Genomics 12: 4. doi: 10.1186/1471-2164-12-4.
33. Cibrián-Jaramillo, A. & Martienssen, R.A. 2009. Darwin's "abominable mystery": The role of RNA interference in the evolution of flowering plants. Cold Spring Harbor Symp. Quant. Biol. 74: 267-273.
34. Committee on Science and Technology. 2008. Systematics and taxonomy: Follow-up. House of Lords Report. London: The Stationery Office.
35. Cronn, R., Liston, A., Parks, M., Gernandt, D.S., Shen, R. & Mockler, T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucl. Acids Res. 36: e122. doi: 10.1093/nar/gkn502.
36. Csencsics, D., Brodbeck, S. & Holderegger, R. 2010. Cost-effective, species-specific microsatellite development for the endangered dwarf bulrush (Typha minima) using next-generation sequencing technology. J. Heredity 101: 789-793.
37. De Groot, G.A., During, H.J., Maas, J.W., Schneider, H., Vogel, J.C. & Erkens, R.H. 2011. Use of rbcl and trnl-f as a two-locus DNA barcode for identification of NW-European ferns: An ecological perspective. PLoS One 6: e16371. doi: 10.1371/journal. pone.0016371.
38. De Queiroz, K. 2007. Species concepts and species delimitation. Syst. Biol. 56: 879-886.
39. DeSalle, R., Egan, M. & Siddall, M. 2005. The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philos. Trans., Ser. B 360: 1905-1916.
40. Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D., Kurtz, S., Lushbough, C. & Brendel, V. 2005. Comparative plant genomics resources at plantGDB. Pl. Physiol. 139: 610-618.
41. Doyle, J.J., 1997 Trees within trees: Genes and species, molecules and morphology. Syst Biol. 46: 537-553
42. Drummond, A.A., B. Buxton, S. Cheung, M. Cooper, A. Heled, J. Kearse, M. Moir, R. Stones-Havas, S. Sturrock, S. Thierer, T. & Wilson, A., 2010 Geneious, version 5.1. http://www.geneious.com.
43. Duarte, J.M., Wall, P.K., Edger, P.P., Landherr, L.L., Ma, H., Pires, J.C., Leebens-Mack, J. & Depamphilis, C.W. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels. B. M. C. Evol. Biol. 10: 61. doi: 10.1186/1471-2148-10-61.
44. Edelist, C., Raffoux, X., Falque, M., Dillmann, C., Sicard, D., Rieseberg, L.H. & Karrenberg, S. 2009. Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae). Amer. J. Bot. 96: 1830-1838.
45. Emerson, K.J., Merz, C.R., Catchen, J.M., Hohenlohe, P.A., Cresko, W.A., Bradshaw, W.E. & Holzapfel, C.M. 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A. 107: 16196-16200.
46. Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M. & Hannon, G.J. 2009. DNA sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res. 19: 1243-1253.
47. Faircloth, B.C. 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus-specific primer design. Molec. Ecol. Resources 8: 92-94.
48. Feuillet, C., Leach, J.E., Rogers, J., Schnable, P. & Eversole, K. 2010. Crop genome sequencing: Lessons and rationales. Trends Pl. Sci. 16: 77-88.
49. Fullwood, M.J., Wei, C.-L., Liu, E.T. & Ruan, Y. 2009. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 19: 521-532.
50. Galan, M., Guivier, E., Caraux, G., Charbonnel, N. & Cosson, J. 2010. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. B. M. C. Genomics 11: 296. doi: 10.1186/1471-2164-11-296.
51. Garvin, M.R., Saitoh, K. & Gharrett, A.J. 2010. Application of single nucleotide polymorphisms to non-model species: A technical review. Molec. Ecol. Resources 10: 915-934.
52. Geraldes, A., Pang, J., Thiessen, N., Cezard, T., Moore, R., Zhao, Y., Tam, A., Wang, S., Friedmann, M., Birol, I., Jones, S.J.M., Cronk, Q.C.B. & Douglas, C.J. 2011 SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molec. Ecol. Resources 11: 81-92
53. Gernandt, D.S., Lopez, G.G., Garcia, S.O. & Liston, A. 2005. Phylogeny and classifcation of Pinus. Taxon 54: 29-42.
54. Giancola, S., Mckhann, H.I., Bérard, A., Camilleri, C., Durand, S., Libeau, P., Roux, F., Reboud, X., Gut, I.G. & Brunel, D. 2006. Utilization of the three high-throughput SNP genotyping methods, the good assay, amplifluor and taqman, in diploid and polyploid plants. Theor. Appl. Genet. 112: 1115-1124.
55. Glenn, T.C. 2011 Field guide to next-generation DNA sequencers. Molec. Ecol. Resources 11: 759-769.
56. Gnerre, S., Maccallum, I., Przybylski, D., Ribeiro, F.J., Burton, J.N., Walker, B.J., Sharpe, T., Hall, G., Shea, T.P., Sykes, S., Berlin, A.M., Aird, D., Costello, M., Daza, R., Williams, L., Nicol, R., Gnirke, A., Nusbaum, C., Lander, E.S. & Jaffe, D.B. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U.S.A. 108: 1513-1518.
57. Godfray, H.C.J. & Knapp, S. 2004. Introduction: Taxonomy for the twenty first century. Philos. Trans., Ser. B 359: 559-569.
58. Gonzalez, M., Baraloto, C., Engel, J., Mori, S., Pétronelli, P., Riéra, B., Roger, A., Thébaud, C., Chave, J. & Hector, A. 2009. Identification of Amazonian trees with DNA barcodes. PLoS One 4: e7483. doi: 10.1371/journal.pone.0007483.
59. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., Di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N. & Regev, A. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29: 644-652.
60. Grattapaglia, D., Silva-Junior, O.B., Kirst, M., de Lima, B.M., Faria, D.A. & Pappas, G.J., Jr. 2011. High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: Assay success, polymorphism and transferability across species. B. M. C. Pl. Biol. 11: 65. DOI: 10.1186/1471-2229-11-65.
61. Griffin, P., Robin, C. & Hoffmann, A. 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. B. M. C. Biol. 9: 19. DOI: 10.1186/1741-7007-9-19.
62. Guo, H., Wang, W., Yang, N., Guo, B., Zhang, S., Yang, R., Yuan, Y., Yu, J., Hu, S. & Sun, Q. 2010. DNA barcoding provides distinction between Radix astragali and its adulterants. Sci. China, C 53: 992-999.
63. Hajibabaei, M., Singer, G.A., Clare, E.L. & Hebert, P.D. 2007. Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. B. M. C. Biol. 5: 24. DOI: 10.1186/1741-7007-5-24.
64. Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S. & Frazer, K.A. 2009. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10: R32. DOI: 10.1186/gb-2009-10-3-r32.
65. Hart, M.W. 2010. The species concept as an emergent propery of population biology. Evolution 65: 613-616.
66. Hartman, A.L., Riddle, S., McPhillips, T., Ludascher, B. & Eisen, J.A. 2010. Introducing W.A.T.E.R.S.: A workflow for the alignment, taxonomy, and ecology of ribosomal sequences. B. M. C. Bioinf. 11: 317. DOI: 10.1186/1471-2105-11-317.
67. Hendry, A.P., Lohmann, L.C.G., Conti, E., Cracraft, J., Crandall, K.A., Faith, D.P., Hã, C., Joly, C.A., Kogure, K., Larigauderie, A., Magallon, S., Moritz, C., Tillier, S., Zardoya, R., Prieur-Richard, A.H.L.N., Walther, B.A., Yahara, T. & Donoghue, M.J. 2010. Evolutionary biology in biodiversity science, conservation and policy: A call to action. Evolution 64: 1-12.
68. Hey, J. 2010. Isolation with migration models for more than two populations. Molec. Biol. Evol. 27: 905-920.
69. Hittinger, C.T., Johnston, M., Tossberg, J.T. & Rokas, A. 2010. Leveraging skewed transcript abundance by RNA-seq to increase the genomic depth of the tree of life. Proc. Natl. Acad. Sci. U.S.A. 107: 1476-1481.
70. Hodges, S.A. & Derieg, N.J. 2009. Adaptive radiations: From field to genomic studies. Proc. Natl. Acad. Sci. U.S.A. 106(Suppl 1): 9947-9954.
71. Hohenlohe, P.A., Bassham, S., Etter, P.D., Stiffler, N., Johnson, E.A. & Cresko, W.A. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6: e1000862. DOI: 10.1371/journal.pgen.1000862.
72. Hollingsworth, P.M., Graham, S.W. & Little, D.P. 2011. Choosing and using a plant DNA barcode. PLoS One 6: e19254. DOI: 10.1371/journal.pone.0019254.
73. Hu, T.T., Pattyn, P., Bakker, E.G., Cao, J., Cheng, J.F., Clark, R.M., Fahlgren, N., Fawcett, J.A., Grimwood, J., Gundlach, H., Haberer, G., Hollister, J.D., Ossowski, S., Ottilar, R.P., Salamov, A.A., Schneeberger, K., Spannagl, M., Wang, X., Yang, L., Nasrallah, M.E., Bergelson, J., Carrington, J.C., Gaut, B.S., Schmutz, J., Mayer, K.F., Van de Peer, Y., Grigoriev, I.V., Nordborg, M., Weigel, D. & Guo, Y.L. 2010. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43: 476-481.
74. Jewell, E., Robinson, A., Savage, D., Erwin, T., Love, C.G., Lim, G.A., Li, X., Batley, J., Spangenberg, G.C. & Edwards, D. 2006. SSRprimer and SSR taxonomy tree: Biome SSR discovery. Nucl. Acids Res. 34: W656-W659.
75. Juenger, T.E., Sen, S., Bray, E., Stahl, E., Wayne, T., McKay, J. & Richards, J.H. 2010. Exploring genetic and expression differences between physiologically extreme ecotypes: Comparative genomic hybridization and gene expression studies of kas-1 and tsu-1 accessions of Arabidopsis thaliana. Pl. Cell Environm. 33: 1268-1284.
76. Keller, A., Harz, C., Matzas, M., Meder, B., Katus, H.A., Ludwig, N., Fischer, U. & Meese, E. 2010. Identification of novel SNPs in glioblastoma using targeted resequencing. PLoS One 6: e18158. DOI: 10.1371/journal.pone.0018158.
77. Kesanakurti, P.R., Fazekas, A.J., Burgess, K.S., Percy, D.M., Newmaster, S.G., Graham, S.W., Barrett, S.C., Hajibabaei, M. & Husband, B.C. 2011. Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Molec. Ecol. 20: 1289-1302.
78. King, I. 2009. The need for the incorporation of phylogeny in the measurement of biological diversity, with special reference to ecosystem functioning research. Bioessays 31: 107-116.
79. Kosakovsky Pond, S., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W.-Y., Taylor, J. & Nekrutenko, A. 2009. Windshield splatter analysis with the galaxy metagenomic pipeline. Genome Res. 19: 2144-2153.
80. Kozarewa, I. & Turner, D.J. 2011. 96-plex molecular barcoding for the Illumina genome analyzer. Meth. Molec. Biol. 733: 279-298.
81. Kramer, E.M. & Hodges, S.A. 2010. Aquilegia as a model system for the evolution and ecology of petals. Philos. Trans., Ser B 365: 477-490.
82. Kress, W., Erickson, D., Jones, F., Swenson, N., Perez, R., Sanjur, O. & Bermingham, E. 2009. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc. Natl. Acad. Sci. U.S.A. 106: 18621-18626.
83. Kress, W.J., Erickson, D.L., Swenson, N.G., Thompson, J., Uriarte, M. & Zimmerman, J.K. 2010. Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot. PLoS One 5: e15409. DOI: 10.1371/journal.pone.0015409.
84. Leavitt, S.D., Johnson, L.A., Goward, T. & St. Clair, L.L. 2011. Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Molec. Phylogenet. Evol. 60: 317-332.
85. Leclercq, S., Rivals, E. & Jarne, P. 2007. Detecting microsatellites within genomes: Significant variation among algorithms. B. M. C. Bioinf. 8: 125. DOI: 10.1186/1471-2105-8-125.
86. Leseberg, C.H. & Duvall, M.R. 2009. The complete chloroplast genome of Coix lacryma-jobi and a comparative molecular evolutionary analysis of plastomes in cereals. J. Molec. Evol. 69: 311-318.
87. Levin, R.A., Whelan, A. & Miller, J.S. 2009. The utility of nuclear conserved ortholog set II (COS II) genomic regions for specieslevel phylogenetic inference in Lycium (Solanaceae). Molec. Phylogenet. Evol. 53: 881-890.
88. Li, H. & Homer, N. 2010. A survey of sequence alignment algorithms for next-generation sequencing. Briefings Bioinf. 11: 473-483.
89. Li, X., Wu, H.X. & Southerton, S.G. 2010. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants. B. M. C. Evol. Biol. 10: 190. DOI: 10.1186/1471-2148-10-190.
90. Lim, G.S., Balke, M. & Meier, R. 2011. Determining species boundaries in a world full of rarity: Singletons, species delimitation methods. Syst. Biol. 60: 1-5.
91. Linnarsson, S. 2010. Recent advances in DNA sequencing methods- general principles of sample preparation. Exp. Cell Res. 316: 1339-1343
92. Liu, L. 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542-2543.
93. Lughadha, E.N., Baillie, J., Barthlott, W., Brummitt, N.A., Cheek, M.R., Farjon, A., Govaerts, R., Hardwick, K.A., Hilton-Taylor, C., Meagher, T.R., Moat, J., Mutke, J., Paton, A.J., Pleasants, L.J., Savolainen, V., Schatz, G.E., Smith, P., Turner, I., Wyse- Jackson, P. & Crane, P.R. 2005. Measuring the fate of plant diversity: Towards a foundation for future monitoring and opportunities for urgent action. Philos. Trans., Ser. B 360: 359-372.
94. McPherson, J.D. 2009. Next-generation gap. Nature, Meth. 6: S2-S5.
95. Meglecz, E., Costedoat, C., Dubut, V., Gilles, A., Malausa, T., Pech, N. & Martin, J.F. 2010. QDD: A user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26: 403-4.
96. Mellmann, A., Harmsen, D., Cummings, C.A., Zentz, E.B., Leopold, S.R., Rico, A., Prior, K., Szczepanowski, R., Ji, Y., Zhang, W., McLaughlin, S.F., Henkhaus, J.K., Leopold, B., Bielaszewska, M., Prager, R., Brzoska, P.M., Moore, R.L., Guenther, S., Rothberg, J.M. & Karch, H. 2011. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One 6: e22751. DOI: 10.1371/journal.pone.0022751.
97. Metzker, M.L. 2009. Sequencing technologies-the next generation. Nat. Rev. Genet. 11: 31-46.
98. Meudt, H.M., Lockhart, P.J. & Bryant, D. 2009. Species delimitation and phylogeny of a New Zealand plant species radiation. B. M. C Evol. Biol. 9: 111. DOI: 10.1186/1471-2148-9-111.
99. Mikheyev, A., Vo, T., Wee, B., Singer, M., Parmesan, C. & Hansson, B. 2010. Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: Performance and a comparison with AFLP-derived distances. PLoS One 5: e11212. DOI: 10.1371/jour nal.pone.0011212.
100. Miller, J.R., Koren, S. & Sutton, G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-27.
101. Miller, W., Hayes, V., Ratan, A., Petersen, D.C., Wittekindt, N.E., Miller, J., Walenz, B., Knight, J., Qi, J., Zhao, F., Wang, Q., Bedoya-Reina, O.C., Katiyar, N., Tomsho, L.P., Kasson, L.M., Hardie, R.A., Woodbridge, P., Tindall, E.A., Bertelsen, M.F., Dixon, D., Pyecroft, S., Helgen, K.M., Lesk, A.M., Pringle, T.H., Patterson, N., Zhang, Y., Kreiss, A., Woods, G.M., Jones, M.E., Schuster, S.C. 2011. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proc. Natl. Acad. Sci. U.S.A. 108: 2348-2353
102. Miwa, H., Odrzykoski, I.J., Matsui, A., Hasegawa, M., Akiyama, H., Jia, Y., Sabirov, R., Takahashi, H., Boufford, D.E. & Murakami, N. 2009. Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes). Gene 441: 169-75.
103. Monaghan, M.T., Wild, R., Elliot, M., Fujisawa, T., Balke, M., Inward, D.J.G., Lees, D.C., Ranaivosolo, R., Eggleton, P., Barraclough, T.G. & Vogler, A.P. 2009. Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Syst. Biol. 58: 298-311.
104. Moore, M.J., Bell, C.D., Soltis, P.S. & Soltis, D.E. 2007. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc. Natl. Acad. Sci. U.S.A. 104: 19363-199368.
105. Moore, M.J., Soltis, P.S., Bell, C.D., Burleigh, J.G. & Soltis, D.E. 2010. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of Eudicots. Proc. Natl. Acad. Sci. U.S.A. 107: 4623-4628.
106. Moritz, C. & Cicero, C. 2004. DNA barcoding: Promise and pitfalls. PLoS Biol. 2: e354. DOI: 10.1371/journal.pbio.0020354.
107. Muellner, A.N., Schaefer, H. & Lahaye, R. 2011. Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae). Molec. Ecol. Resources 11: 450-460.
108. Myles, S., Boyko, A.R., Owens, C.L., Brown, P.J., Grassi, F., Aradhya, M.K., Prins, B., Reynolds, A., Chia, J.M., Ware, D., Bustamante, C.D. & Buckler, E.S. 2011 Genetic structure and domestication history of the grape. Proc. Natl. Acad. Sci. U.S.A. 108: 3530-3535
109. Ness, R.W., Siol, M. & Barrett, S.C. 2011 De novo sequence assembly and characterisation of the floral transcriptome in crossand self-fertilizing plants. B. M. C. Genomics 7: 298-315. DOI: 10.1186/1471-2164-12-298.
110. Nielsen, R., Paul, J.S., Albrechtsen, A. & Song, Y.S. 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443-451.
111. Parchman, T., Geist, K., Grahnen, J., Benkman, C. & Buerkle, C. 2010. Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. B. M. C. Genomics 11: 180. DOI: 10.1186/1471-2164-11-180.
112. Parks, M., Cronn, R. & Liston, A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. B. M. C. Biol. 7: 84. DOI:10.1186/1741-7007-7-84.
113. Pennisi, E. 2010. Genomics: Semiconductors inspire new sequencing technologies. Science 327: 1190.
114. Piredda, R., Simeone, M.C., Attimonelli, M., Bellarosa, R. & Schirone, B. 2011. Prospects of barcoding the Italian wild dendroflora: Oaks reveal severe limitations to tracking species identity. Molec. Ecol. Resources 11: 72-83.
115. Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y. & Vandepoele, K. 2009. Plaza: A comparative genomics resource to study gene and genome evolution in plants. Pl. Cell 21: 3718-3731.
116. Quesada, T., Li, Z., Dervinis, C., Li, Y., Bocock, P.N., Tuskan, G.A., Casella, G., Davis, J.M. & Kirst, M. 2008. Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytol. 180: 408-420.
117. Ragupathy, S., Newmaster, S.G., Murugesan, M. & Balasubramaniam, V. 2009. DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Molec. Ecol. Resources 9(Suppl S1): 164-171.
118. Ratnakumar, A., McWilliam, S., Barris, W. & Dalrymple, B.P. 2010. Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes. B. M. C. Genomics 11: 458. DOI: 10.1186/1471-2164-11-458.
119. Reeves, P.A. & Richards, C.M. 2011. Species delimitation under thegeneral lineage concept: An empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Syst. Biol. 60: 45-59.
120. Rieseberg, L. & Willis J.H. 2007. Plant speciation. Science 317: 910.
121. Rodrigue, S., Materna, A.C., Timberlake, S.C., Blackburn, M.C., Malmstrom, R.R., Alm, E.J. & Chisholm, S.W. 2010. Unlocking short read sequencing for metagenomics. PLoS One 5: e11840. DOI: 10.1371/journal.pone.0011840.
122. Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N.J., Hentschke, M., Chen, W., Pu, F., Peng, Y., Li, J., Xi, F., Li, S., Li, Y., Zhang, Z., Yang, X., Zhao, M., Wang, P., Guan, Y., Cen, Z., Zhao, X., Christner, M., Kobbe, R., Loos, S., Oh, J., Yang, L., Danchin, A., Gao, G.F., Song, Y., Li, Y., Yang, H., Wang, J., Xu, J., Pallen, M.J., Wang, J., Aepfelbacher, M., Yang, R. & the E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium. 2011. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. New England J. Med., online publication. DOI: 10.1056/NEJMoa1107643.
123. Rokas, A. & Abbot, P. 2009. Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200.
124. Rothberg, J.M., Hinz, W., Rearick, T.M., Schulttz, J., Mileski, W., Davey, M., Leamon, J.H., Johnson, K., Milgrew, M.J., Edwards, M., Hoon, J., Simons, J.F., Marran, D., Myers, J.W., Davidson, J.F., Branting, A., Nobile, J.R., Puc, B.P., Light, D., Clark, T.A., Huber, M., Branciforte, J.T., Stoner, I.B., Cawley, S.E., Lyons, M., Fu, Y., Homer, N., Sedova, M., Miao, X., Reed, B., Sabina, J., Feierstein, E., Schorn, M., Alanjary, M., Dimalanta, E., Dressman, D., Kasinskas, R., Sokolsky, T., Fidanza, J.A., Namsaraev, E., McKernan, K.J., Williams, A., Roth, G.T. & Bustillo, J. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352
125. Roy, S., Tyagi, A., Shukla, V., Kumar, A., Singh, U.M., Chaudhary, L.B., Datt, B., Bag, S.K., Singh, P.K., Nair, N.K., Husain, T. & Tuli, R. 2010. Universal plant DNA barcode loci may not work in complex groups: A case study with Indian Berberis species. PLoS One 5: e13674. DOI: 10.1371/journal.pone.0013674.
126. Sanger, F., Nicklen, S. & Coulson, A.R. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 74: 5463-5467.
127. Santana, Q., Coetzee, M., Steenkamp, E., Mlonyeni, O., Hammond, G., Wingfield, M. & Wingfield, B. 2009. Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques 46: 217-223.
128. Scascitelli, M., Whitney, K.D., Randell, R.A., King, M., Buerkle, C.A. & Rieseberg, L.H. 2011. Genome scan of hybridizing sunflowers from Texas (Helianthus annuus and H. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation. Molec. Ecol. 19: 521-541.
129. Schloss, J.A. 2008. How to get genomes at one ten-thousandth the cost. Nat. Biotechnol. 26: 1113-1115.
130. Schwarz-Sommer, Z., de Andrade Silva, E., Berndtgen, R., Lonnig, W.E., Muller, A., Nindl, I., Stuber, K., Wunder, J., Saedler, H., Gubitz, T., Borking, A., Golz, J.F., Ritter, E. & Hudson, A. 2003. A linkage map of an F2 hybrid population of Antirrhinum majus and A. molle. Genetics 163: 699-710.
131. Schwarz-Sommer, Z., Gubitz, T., Weiss, J., Gomez-di-Marco, P., Delgado-Benarroch, L., Hudson, A. & Egea-Cortines, M. 2010. A molecular recombination map of Antirrhinum majus. B. M. C. Pl. Biol. 10: 275. DOI: 10.1186/1471-2229-10-275.
132. Seeb, J.E., Carvalho, G., Hauser, L., Naish, K., Roberts, S. & Seeb, L.W. 2011. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molec. Ecol. Resources 11: 1-8.
133. Shi, T., Huang, H. & Barker, M.S. 2010. Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related ericales. Ann. Bot. 106: 497-504.
134. Shinozaki, K., Deno, H., Wakasugi, T. & Sugiura, M. 1986. Tobacco chloroplast gene coding for subunit I of proton-translocating ATPase: Comparison with the wheat subunit I and E. coli subunit B. Curr. Genet. 10: 421-423.
135. Slate, J., Gratten, J., Beraldi, D., Stapley, J., Hale, M. & Pemberton, J.M. 2009. Gene mapping in the wild with SNPs: Guidelines and future directions. Genetica 136: 97-107.
136. Slotte, T., Foxe, J.P., Hazzouri, K.M. & Wright, S.I. 2010. Genomewide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Molec. Biol. Evol. 27: 1813-1821.
137. Smith, A.M., Heisler, L.E., St. Onge, R.P., Farias-Hesson, E., Wallace, I.M., Bodeau, J., Harris, A.N., Perry, K.M., Giaever, G., Pourmand, N. & Nislow, C. 2010. Highly-multiplexed barcode sequencing: An efficient method for parallel analysis of pooled samples. Nucl. Acids Res. 38: e142. DOI: 10.1093/nar/gkq368.
138. Sobel, J.M., Chen, G.F., Watt, L.R. & Schemske, D.W. 2010. The biology of speciation. Evolution 64: 295-315.
139. Soltis, D.E., Albert, V.A., Leebens-Mack, J., Palmer, J.D., Wing, R.A., dePamphilis, C.W., Ma, H., Carlson, J.E., Altman, N., Kim, S., Wall, P.K., Zuccolo, A. & Soltis, P.S. 2008. The Amborella genome: An evolutionary reference for plant biology. Genome Biol. 9: 402. DOI: 10.1186/gb-2008-9-3-402.
140. Soltis, D.E., Burleigh, G., Barbazuk, W.B., Moore, M.J. & Soltis, P.S. 2010. Advances in the use of next-generation sequence data in plant systematics and evolution. Acta. Hort. 859: 193-206.
141. Song, B.H. & Mitchell-Olds, T. 2011. Evolutionary and ecological genomics of non-model plants. J. Syst. Evol. 49: 17-24.
142. Sønstebø, J.H., Gielly, L., Brysting, A.K., Elven, R., Edwards, M., Haile, J., Willerslev, E., Coissac, E., Rioux, D., Sannier, J., Taberlet, P. & Brochmann, C. 2010. Using next-generation sequencing for molecular reconstruction of past arctic vegetation and climate. Molec. Ecol. Resources 10: 1009-1018.
143. Squirrell, J. & Hollingsworth, P. 2003. How much effort is required to isolate nuclear microsatellites from plants? Molec. Ecol. 12: 1339-1348.
144. Stapley, J., Reger, J., Feulner, P.G.D., Smadja, C., Galindo, J., Ekblom, R., Bennison, C., Ball, A.D., Beckerman, A.P. & Slate, J. 2010. Adaptation genomics: The next generation. Trends Ecol. Evol. 12: 702-712
145. Suzuki, S., Ono, N., Furusawa, C., Ying, B.-W. & Yomo, T. 2011. Comparison of sequence reads obtained from three next-generation sequencing platforms. PLoS One 6: e19534. DOI: 10.1371/journal.pone.0019534.
146. Syring, J., Farrell, K., Businsky, R., Cronn, R. & Liston, A. 2007 Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus. Syst. Biol. 56: 163-181
147. Tang, H., Bowers, J.E., Wang, X. & Paterson, A.H. 2010. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc. Natl. Acad. Sci. U.S.A. 107: 472-477.
148. Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M. & Paterson, A.H. 2008. Unraveling ancient hexaploidy through multiplyaligned angiosperm gene maps. Genome Res. 18: 1944-1954.
149. Tautz, D., Ellegren, H. & Weigel, D. 2010. Next generation molecular ecology. Molec. Ecol. 19 Suppl. s1: 1-3.
150. Tavares, R., Cagnon, M., Negrutiu, I. & Mouchiroud, D. 2010. Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms. B. M. C. Evol. Biol. 10: 240. DOI: 10.1186/1471-2148-10-240.
151. Telle, S. & Thines, M. 2008. Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases. PLoS One 3: e3584. DOI: 10.1371/journal.pone.0003584.
152. Timme, R.E. & Delwiche, C.F. 2010. Uncovering the evolutionary origin of plant molecular processes: Comparison of Coleochaete (coleochaetales) and Spirogyra (zygnematales) transcriptomes. B. M. C. Pl. Biol. 10: 96. DOI: 10.1186/1471-2229-10-96.
153. Timp, W., Mirsaidov, U.M., Wang, D., Comer, J., Aksimentiev, A. & Timp, G. 2010. Nanopore sequencing: Electrical measurements of the code of life. I. E. E. E. Trans. Nanotechnol. 9: 281-294.
154. Vendramin, E., Dettori, M.T., Giovinazzi, J., Micali, S., Quarta, R. & Verde, I. 2007. A set of ESTs-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species. Molec. Ecol. Notes 7: 307-310.
155. Vera, J.C., Wheat, C.W., Fescemyer, H.W., Frilander, M.J., Crawford, D.L., Hanski, I. & Marden, J.H. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molec. Ecol. 17: 1636-1647.
156. Voelckel, C., Borevitz, J.O., Kramer, E.M. & Hodges, S.A. 2011. Within and between whorls: Comparative transcriptional profiling of Aquilegia and Arabidopsis. PLoS One 5: e9735. DOI: 10.1371/journal.pone.0009735.
157. Wall, P.K., Leebens-Mack, J., Chanderbali, A.S., Barakat, A., Wolcott, E., Liang, H., Landherr, L., Tomsho, L.P., Hu, Y., Carlson, J.E., Ma, H., Schuster, S.C., Soltis, D.E., Soltis, P.S., Altman, N. & dePamphilis, C.W. 2009. Comparison of next generation sequencing technologies for transcriptome characterization. B. M. C. Genomics 10: 347. DOI: 10.1186/1471-2164-10-347.
158. Wang, W.K., Ho, C.W., Hung, K.H., Wang, K.H., Huang, C.C., Araki, H., Hwang, C.C., Hsu, T.W., Osada, N. & Chiang, T.Y. 2010. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: Evidence of genome-wide admixture. New Phytol. 188: 488-500.
159. Waterhouse, R.M., Zdobnov, E.M., Tegenfeldt, F., Li, J. & Kriventseva, E.V. 2011. OrthoDB: The hierarchical catalog of eukaryotic orthologs in 2011. Nucl. Acids Res. 39: D283-D288.
160. Wheat, C.W. 2010. Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 138: 433-451.
161. Will, K.W. & Rubinoff, D. 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20: 47-55.
162. Willyard, A., Cronn, R. & Liston, A. 2009. Reticulate evolution and incomplete lineage sorting among the ponderosa pines. Molec. Phylogenet. Evol. 52: 498-511.
163. Wilson, Y. & Hudson, A. 2011. The evolutionary history of Antirrhinum suggests that ancestral phenotype combinations survived repeated hybridizations. Plant J. 66: 1032-43.
164. Wolf, P.G., Der, J.P., Duffy, A.M., Davidson, J.B., Grusz, A.L. & Pryer, K.M. 2010. The evolution of chloroplast genes and genomes in ferns. Pl. Molec. Biol. 76: 251-261.
165. Wu, C.A., Lowry, D.B., Cooley, A.M., Wright, K.M., Lee, Y.W. & Willis, J.H. 2008. Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity 100: 220-230.
166. Wu, F., Eannetta, N.T., Xu, Y., Plieske, J., Ganal, M., Pozzi, C., Bakaher, N. & Tanksley, S.D. 2010. Cosii genetic maps of two diploid Nicotiana species provide a detailed picture of synteny with tomato and insights into chromosome evolution in tetraploid N. tabacum. Theor. Appl. Genet. 120: 809-827.
167. Yang, M., Zhang, X., Liu, G., Yin, Y., Chen, K., Yun, Q., Zhao, D., Al-Mssallem, I.S. & Yu, J. 2010. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5: e12762. DOI: 10.1371/journal.pone.0012762.
168. Yu, Z., Haberer, G., Matthes, M., Rattei, T., Mayer, K.F.X., Gierl, A. & Torres-Ruiz, R.A. 2010. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 107: 17809-17814.
169. Zeng, Y.F., Liao, W.J., Petit, R.J. & Zhang, D.Y. 2010 Exploring species limits in two closely related Chinese oaks. PLoS One 5: e15529. DOI: 10.1371/journal.pone.0015529.
170. Zhang, W., Chen, J., Yang, Y., Tang, Y., Shang, J. & Shen, B. 2011. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS One 6: e17915. DOI: 10.1371/journal.pone.0017915.
171. Zhong, B., Yonezawa, T., Zhong, Y. & Hasegawa, M. 2010. The position of Gnetales among seed plants: Overcoming pitfalls of chloroplast phylogenomics. Molec. Biol. Evol. 27: 2855-2863.
172. Zoschke, R., Liere, K. & Borner, T. 2007. From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. Plant J. 50: 710-722.