Why size really matters when sequencing plant genomes

Plant Ecology and Diversity

Volumn 5, Issue 4, 2012, Pages 415-425

  Kelly, Laura J ^a,b   Leitch, Andrew R ^a   Fay, Michael F ^b   Renny Byfield, Simon ^a   Pellicer, Jaume ^b   Macas, Jiří ^c   Leitch, Ilia J ^b  

^a QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^b JODRELL LABORATORY   (United Kingdom)

^c INSTITUTE OF PLANT MOLECULAR BIOLOGY   (Czech Republic)

Author keywords

C value; genome assembly; genome sequencing; genome size evolution; land plants; next generation sequencing; second generation sequencing; third generation sequencing

Indexed keywords

EMBRYOPHYTA;

EID: 84871966941     PISSN: 17550874     EISSN: 17551668     Source Type: Journal    
DOI: 10.1080/17550874.2012.716868     Document Type: Article

References (95)

1. Alkan, C, Sajjadian, S and Eichler, EE. 2011. Limitations of next-generation genome sequence assembly. Nature Methods, 8: 61-65.
2. Ambrožová, K, Mandáková, T, Bureš, P, Neumann, P, Leitch, IJ, Koblížková, A, Macas, J and Lysák, MA. 2011. Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies. Annals of Botany, 107: 255-268.
3. APG III. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, 161: 105-121.
4. Arumuganathan, K and Earle, ED. 1991. Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9: 208-218.
5. Baker, M. 2012. De novo genome assembly: what every biologist should know. Nature Methods, 9: 333-337.
6. Banks, JA, Nishiyama, T, Hasebe, M, Bowman, JL, Gribskov, M, dePamphilis, C, Albert, VA, Aono, N, Aoyama, TAmbrose, BA. 2011. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 332: 960-963.
7. Barker, MS and Wolf, PG. 2010. Unfurling fern biology in the genomics age. Bioscience, 60: 177-185.
8. Barthelson, R, McFarlin, AJ, Rounsley, SD and Young, S. 2011. Plantagora: modelling whole genome sequencing and assembly of plant genomes. PLoS ONE, 6: e28436
9. Bennett, MD and Leitch, IJ. 2005a. "Genome size evolution in plants". In The evolution of the genome, Edited by: Gregory, TR. 89-162. Amsterdam: Elsevier Academic Press.
10. Bennett, MD and Leitch, IJ. 2005b. Nuclear DNA amounts in angiosperms-progress, problems and prospects. Annals of Botany, 95: 45-90.
11. Bennett MD, Leitch IJ. 2010. Plant DNA C-values database. Release 5.0, Dec. 2010 http://www.kew.org/cvalues/ (http://www.kew.org/cvalues/)
12. Bennett, MD, Leitch, IJ, Price, HJ and Johnston, JS. 2003. Comparisons with Caenorhabditis (ε100 Mb) and Drosophila (ε175 Mb) using flow cytometry show genome size in Arabidopsis to be ε157 Mb and thus ε25 % larger than the Arabidopsis Genome Initiative estimate of ε125 Mb. Annals of Botany, 91: 547-557.
13. Bennett, MD and Smith, JB. 1976. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society London B: Biological Sciences, 274: 227-274.
14. Bennett, MD and Smith, JB. 1991. Nuclear DNA amounts in angiosperms. Philosophical Transactions of the Royal Society London B: Biological Sciences, 334: 309-345.
15. Bennetzen, JL, Schmutz, J, Wang, H, Percifield, R, Hawkins, J, Pontaroli, AC, Estep, M, Feng, L, Vaughn, JNGrimwood, J. 2012. Reference genome sequence of the model plant Setaria. Nature Biotechnology, 30: 555-561.
16. Cao, J, Schneeberger, K, Ossowski, S, Günther, T, Bender, S, Fitz, J, Koenig, D, Lanz, C, Stegle, OLippert, C. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics, 43: 956-963.
17. Chain, PSG, Grafham, DV, Fulton, RS, FitzGerald, MG, Hostetler, J, Muzny, D, Ali, J, Birren, B, Bruce, DCBuhay, C. 2009. Genome project standards in a new era of sequencing. Science, 326: 236-237.
18. Dassanayake, M, Oh, DH, Haas, JS, Hernandez, A, Hong, H, Ali, S, Yun, DJ, Bressan, RA, Zhu, JKBohnert, HJ. 2011. The genome of the extremophile crucifer Thellungiella parvula. Nature Genetics, 43: 913-918.
19. Doyle, JJ and Luckow, MA. 2003. The rest of the iceberg. Legume evolution and diversity in a phylogenetic context. Plant Physiology, 131: 900-910.
20. Earl, D, Bradnam, K, St John, J, Darling, A, Lin, DW, Fass, J, Hung, OKY, Buffalo, V, Zerbino, DRDiekhans, M. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research, 21: 2224-2241.
21. Feldman, M. 2001. "The origin of cultivated wheat". In The world wheat book, Edited by: Bonjean, AP and Angus, WJ. 3-56. Paris, France: Lavoisier Publishing.
22. Feschotte, F and Pritham, EJ. 2007. DNA transposons and the evolution of eukaryotic genomes. Annual Review of Genetics, 41: 331-368.
23. Feuillet, C, Leach, JE, Rogers, J, Schnable, PS and Eversole, K. 2011. Crop genome sequencing: lessons and rationales. Trends in Plant Science, 16: 77-88.
24. Frodin, DG. 2004. History and concepts of big plant genera. Taxon, 53: 753-776.
25. Glenn, TC. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11: 759-769.
26. Gregory, TR. 2005. Synergy between sequence and size in large-scale genomics. Nature Reviews Genetics, 6: 699-708.
27. Greilhuber, J, Borsch, T, Müller, K, Worberg, A, Porembski, S and Barthlott, W. 2006. Smallest angiosperm genomes found in Lentibulariaceae with chromosomes of bacterial size. Plant Biology, 8: 770-777.
28. Greilhuber, J, Doležel, J, Lysak, MA and Bennett, MD. 2005. The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents. Annals of Botany, 95: 91-98.
29. Grover, CE and Wendel, JE. 2010. Recent insights into mechanisms of genome size change in plants. Journal of Botany, doi:10.1155/2010/382732
30. Hawkins, JS, Kim, HR, Nason, JD, Wing, RA and Wendel, JF. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Research, 16: 1252-1261.
31. Hernandez, P, Martis, M, Dorado, G, Pfeifer, M, Gálvez, S, Schaaf, S, Jouve, N, Šimkova, H, Valárik, MDoležel, J. 2012. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant Journal, 69: 377-386.
32. Hu, TT, Pattyn, P, Bakker, EG, Cao, J, Cheng, JF, Clark, RM, Fahlgren, N, Fawcett, JA, Grimwood, JGundlach, H. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics, 43: 476-481.
33. Huang, S, Li, R, Zhang, Z, Li, L, Gu, XF, Fan, W, Lucas, WJ, Wang, XW, Xie, BYNi, PX. 2009. The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41: 1275-1283.
34. Jackson, S, Rounsley, S and Purugganan, M. 2006. Comparative sequencing of plant genomes: choices to make. The Plant Cell, 18: 1100-1104.
35. Jackson, SA, Iwata, A, Lee, S-H, Schmutz, J and Shoemaker, R. 2011. Sequencing crop genomes: approaches and applications. New Phytologist, 191: 915-925.
36. Jiao, Y, Wickett, NJ, Ayyampalayam, S, Chanderbali, AS, Landherr, L, Ralph, PE, Tomsho, LP, Hu, Y, Liang, HSoltis, PS. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature, 473: 97-100.
37. Kejnovsky, E, Leitch, IJ and Leitch, AR. 2009. Contrasting evolutionary dynamics between angiosperm and mammalian genomes. Trends in Ecology and Evolution, 24: 572-582.
38. Kelly, LJ and Leitch, IJ. 2011. Exploring giant plant genomes with next-generation sequencing technology. Chromosome Research, 19: 939-953.
39. Khandelwal, S. 1990. Chromosome evolution in the genus Ophioglossum L. Botanical Journal of the Linnean Society, 102: 205-217.
40. Kovach, A, Wegrzyn, JL, Parra, G, Holt, C, Bruening, GE, Loopstra, CA, Hartigan, J, Yandell, M, Langley, CHKorf, I. 2010. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, 11: 420
41. Lai, JS, Li, RQ, Xu, X, Jin, WW, Xu, ML, Zhao, HN, Xiang, ZK, Song, WB, Ying, KZhang, M. 2010. Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics, 42: 1027-1030.
42. Lang, D, Zimmer, AD, Rensing, SA and Reski, R. 2008. Exploring plant diversity: the Physcomitrella genome and beyond. Trends in Plant Science, 13: 542-549.
43. Leitch, IJ, Beaulieu, JM, Chase, MW, Leitch, AR and Fay, MF. 2010. Genome size dynamics and evolution in monocots. Journal of Botany, doi:10.1155/2010/862516
44. Leitch, IJ, Kahandawala, I, Suda, J, Hanson, L, Ingrouille, MJ, Chase, MW and Fay, MF. 2009. Genome size diversity in orchids-consequences and evolution. Annals of Botany, 104: 469-481.
45. Leitch, IJ and Leitch, AR. 2012. "Genome size diversity and evolution in land plants". In Plant genome diversity Edited by: Leitch, IJ, Greilhuber, J, Doležel, J and Wendel, JF. editorsvol 2, Physical structure, behaviour and evolution of plant genomes. Vienna (Austria): Springer-Verlag. p. 307-322.
46. Leitch, IJ, Soltis, DE, Soltis, PS and Bennett, MD. 2005. Evolution of DNA amounts across land plants (Embryophyta). Annals of Botany, 95: 207-217.
47. Luo, MC, Deal, KR, Akhunov, ED, Akhunova, AR, Anderson, OD, Anderson, JA, Blake, N, Clegg, MT, Coleman-Derr, DConley, EJ. 2009. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proceedings of the National Academy of Sciences of the United States of America, 106: 15780-15785.
48. Lysák, MA, Koch, MA, Beaulieu, JM, Meister, A and Leitch, IJ. 2009. The dynamic ups and downs of genome size evolution in Brassicaceae. Molecular Biology and Evolution, 26: 85-98.
49. Mabberley, DJ. 2008. Mabberley's plant-book: a portable dictionary of plants, their classifications, and uses, Cambridge, UK: Cambridge University Press.
50. Macas, J, Neumann, P and Navrátilová, A. 2007. Repetitive DNA in pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8: 427
51. Massa, AN, Wanjugi, H, Deal, KR, O'Brien, K, You, FM, Maiti, R, Chan, AP, Gu, YQ, Luo, MCAnderson, OD. 2011. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Molecular Biology and Evolution, 28: 2537-2547.
52. Mishler, BD and Kelch, DG. 2008. "Phylogenomics and early land plant evolution". In Bryophyte biology, 2nd, Edited by: Goffinet, B and Shaw, AJ. 173-198. Cambridge, UK: Cambridge University Press.
53. Morrell, PL, Buckler, ES and Ross-Ibarra, J. 2012. Crop genomics: advances and applications. Nature Reviews Genetics, 13: 85-96.
54. Narayan, RKJ. 1982. Discontinuous DNA variation in the evolution of plant species-the genus Lathyrus. Evolution, 36: 877-891.
55. Neale, DB and Kremer, A. 2011. Forest tree genomics: growing resources and applications. Nature Reviews Genetics, 12: 111-122.
56. Neumann, P, Koblížková, A, Navrátilová, A and Macas, J. 2006. Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics, 173: 1047-1056.
57. O'Brien, IEW, Smith, DR, Gardner, RC and Murray, BG. 1996. Flow cytometric determination of genome size in Pinus. Plant Science, 115: 91-99.
58. Oh, DH, Dassanayake, M, Haas, JS, Kropornika, A, Wright, C, d'Urzo, MP, Hong, H, Ali, S, Hernandez, ALambert, GM. 2010. Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis. Plant Physiology, 154: 1040-1052.
59. Parisod, C, Holderegger, R and Brochmann, C. 2010. Evolutionary consequences of autopolyploidy. New Phytologist, 186: 5-17.
60. Paterson, AH, Freeling, M, Tang, H and Wang, X. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology, 61: 349-372.
61. Pellicer, J, Fay, MF and Leitch, IL. 2010. The largest eukaryotic genome of them all?. Botanical Journal of the Linnean Society, 164: 10-15.
62. Pennisi, E. 2011. Green genomes. Science, 332: 1372-1375.
63. Piegu, B, Guyot, R, Picault, N, Roulin, A, Saniyal, A, Kim, H, Collura, K, Brar, DS, Jackson, SWing, RA. 2006. Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Research, 16: 1262-1269.
64. Pryer, KM, Schneider, H, Zimmer, EA and Banks, JA. 2002. Deciding among green plants for whole genome studies. Trends in Plant Science, 7: 550-554.
65. Renny-Byfield, S, Chester, M, Kovarík, A, Le Comber, SC, Grandbastien, M-A, Deloger, M, Nichols, RA, Macas, J, Novák, PChase, MW. 2011. Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Molecular Biology and Evolution, 28: 2843-2854.
66. Rensing, SA, Lang, D, Zimmer, AD, Terry, A, Salamov, A, Shapiro, H, Nishiyama, T, Perroud, PF, Lindquist, EAKamisugi, Y. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319: 64-69.
67. Ritz, A, Bashir, A and Raphael, BJ. 2010. Structural variation analysis with strobe reads. Bioinformatics, 26: 1291-1298.
68. Salzberg, SL, Phillippy, AM, Zimin, A, Puiu, D, Magoc, T, Koren, S, Treangen, TJ, Schatz, MC, Delcher, ALRoberts, M. 2012. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Research, 22: 557-567.
69. Sato, S, Nakamura, Y, Kaneko, T, Asamizu, E, Kato, T, Nakao, M, Sasamoto, S, Watanabe, A, Ono, AKawashima, K. 2008. Genome structure of the legume, Lotus japonicus. DNA Research, 15: 227-239.
70. Schadt, EE, Turner, S and Kasarskis, A. 2010. A window into third generation sequencing. Human Molecular Genetics, 19: R227-R240.
71. Schatz, MC, Delcher, AL and Salzberg, SL. 2010. Assembly of large genomes using second-generation sequencing. Genome Research, 20: 1165-1173.
72. Schatz, MC, Witkowski, J and McCombie, WR. 2012. Current challenges in de novo plant genome sequencing and assembly. Genome Biology, 13: 243
73. Schmutz, J, Cannon, SB, Schlueter, J, Ma, JX, Mitros, T, Nelson, W, Hyten, DL, Song, QJ, Thelen, JJCheng, JL. 2010. Genome sequence of the palaeopolyploid soybean. Nature, 463: 178-183.
74. Schnable, PS, Ware, D, Fulton, RS, Stein, JC, Wei, FS, Pasternak, S, Liang, CZ, Zhang, JW, Fulton, LGraves, TA. 2009. The B73 maize genome: complexity, diversity and dynamics. Science, 326: 1112-1115.
75. Simpson, JT and Durbin, R. 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Research, 22: 549-556.
76. Soltis, DE, Albert, VA, Leebens-Mack, J, Palmer, JD, Wing, RA, Depamphilis, CW, Ma, H, Carlson, JE, Altman, NKim, S. 2008. The Amborella genome: an evolutionary reference for plant biology. Genome Biology, 9: 402
77. Soltis, DE, Moore, MJ, Burleigh, JG, Bell, CD and Soltis, PS. 2010. Assembling the angiosperm tree of life: progress and future prospects. Annals of the Missouri Botanical Garden, 97: 514-526.
78. Soltis, DE, Smith, SA, Cellinese, N, Wurdack, KJ, Tank, DC, Brockington, SF, Refulio-Rodriguez, NF, Walker, JB, Moore, MJCarlsward, BS. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany, 98: 704-730.
79. Soltis, PS and Soltis, DE. 2012. "Angiosperm phylogeny: a framework for studies of genome evolution". In Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes, Edited by: Leitch, IJ, Greilhuber, J, Doležel, J and Wendel, JF. 1-11. Vienna, Austria: Springer-Verlag.
80. Tatum, TC, Stepanovic, S, Biradar, DP, Rayburn, AL and Korban, SS. 2005. Variation in nuclear DNA content in Malus species and cultivated apples. Genome, 48: 924-930.
81. Temsch, EM, Temsch, W, Ehrendorfer-Schratt, L and Greilhuber, J. 2010. Heavy metal pollution, selection, and genome size: the species of the Žerjav study revisited with flow cytometry. Journal of Botany, doi:10.1155/2010/596542
82. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408: 796-815.
83. The Potato Genome Sequencing Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature, 475: 189-195.
84. The Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485: 635-641.
85. Treangen, TJ and Salzberg, SL. 2012. Repetitive DNA and next-generation sequencing: computational challenges and solution. Nature Review Genetics, 13: 36-46.
86. Varshney, RK, Chen, W, Li, Y, Bharti, AK, Saxena, RK, Schlueter, JA, Donoghue, MTA, Azam, S, Fan, GWhaley, AM. 2012. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology, 30: 83-89.
87. Vrána J, Šimková H, Kubaláková M, Cíhalíková J, Doležel J. 2012. Flow cytometric chromosome sorting in plants: the next generation. Methods http://dx.doi.org/10.1016/j.ymeth.2012.03.006 (http://dx.doi.org/10.1016/j.ymeth.2012.03.006)
88. Wakamiya, I, Newton, RJ, Johnston, JS and Price, HJ. 1993. Genome size and environmental factors in the genus Pinus. American Journal of Botany, 80: 1235-1241.
89. Weigel, D and Mott, R. 2009. The 1001 genomes project for Arabidopsis thaliana. Genome Biology, 10: 107
90. Wicker, T, Buchmann, JP and Keller, B. 2010. Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Research, 20: 1229-1237.
91. Wicker, T, Mayer, KFX, Gundlach, H, Martis, M, Steuernagel, B, Scholz, U, Šimková, H, Kubaláková, M, Choulet, FTaudien, S. 2011. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell, 23: 1706-1718.
92. Wicker, T, Taudien, S, Houben, A, Keller, B, Graner, A, Platzer, M and Stein, N. 2008. A whole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant Journal, 59: 712-722.
93. Young, ND, Debellé, F, Oldroyd, GED, Geurts, R, Cannon, SB, Udvardi, MK, Benedito, VA, Mayer, KFX, Gouzy, JSchoof, H. 2011. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480: 520-524.
94. Zhou, S, Bechner, MC, Place, M, Churas, CP, Pape, L, Leong, SA, Runnheim, R, Forrest, DK, Goldstein, SLivny, M. 2007. Validation of rice genome sequence by optical mapping. BMC Genomics, 8: 278
95. Zhou, S, Wei, F, Nguyen, J, Bechner, M, Konstantinos, P, Goldstein, S, Pape, L, Mehan, MR, Churas, CPasternak, S. 2009. A single molecule scaffold for the maize genome. PLoS Genetics, 5: e1000711