Genome size diversity and evolution in land plants

Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes

Volumn , Issue , 2013, Pages 307-322

  Leitch, Ilia J ^a   Leitch, Andrew R ^b  

^a JODRELL LABORATORY   (United Kingdom)

^b QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84936950105     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1160-4_19     Document Type: Chapter

References (110)

1. Abderrahman SA (2004) Nuclear DNA content of haploid and diploid Physcomitrium pyriforme using DAPI staining. Korean J Genet 26:245-250
2. Abraham A, Ninan CA, Mathew PM (1962) Studies on the cytology and phylogeny of the pteridophytes VII. Observations on one hundred species of South Indian ferns. J Indian Bot Soc 41:339-421
3. APG II (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. Bot J Linn Soc 141:399-436
4. APG III (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105-121
5. Barker MS (2013) Karyotype and genome evolution in pteridophytes. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Wien, pp 245-253
6. Barker MS, Wolf PG (2010) Unfurling fern biology in the genomics age. Bioscience 60:177-185
7. Barker MS, Graham SW, Rieseberg LH (2010) Comparative gymnosperm transcriptomics. Abstract for Botany 2010, http://2010.botany conference.org/engine/search/index.php?func1/4detail&aid1/4437. Accessed on 9 July 2012
8. Barlow BA, Wiens D (1971) The cytogeography of the loranthaceous mistletoes. Taxon 20:291-312
9. Bateman RM, Hilton J, Rudall PJ (2006) Morphological and molecular phylogenetic context of the angiosperms: contrasting the ‘top-down’ and ‘bottom-up’ approaches used to infer the likely characteristics of the first flowers. J Exp Bot 57:3471-3503
10. Bennett MD, Leitch IJ (2010) Plant DNA C-values database (release 5.0, Dec 2010). http://data.kew.org/cvalues/. Accessed on 9 July 2012
11. Bennett MD, Leitch IJ (2011) Nuclear DNA amounts in angiosperms - targets, trends and tomorrow. Ann Bot 107:467-590
12. Blackwood M (1953) Chromosomes of Phylloglossum drummondii. Nature 172:591-592
13. Bornefeld T, Grillenberger C (1987) Some aspects of size in chromosome analysis of liverworts (Marchantiales). Nova Hedwigia 44:91-100
14. Brandes A, Heslop-Harrison JS, Kamm A, Kubis S, Doudrick RL, Schmidt T (1997) Comparative analysis of the chromosomal and genomic organization of Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol Biol 33:11-21
15. Brownsey PJ, Lovis JD (1987) Chromosome numbers of the New Zealand species of Psilotum and Tmesipteris, and the phylogenetic relationships of the Psilotales. New Zealand J Bot 25:439-454
16. Chase MW, Fay MF, Devey DS, Maurin O, Rønsted N et al (2006) Multigene analyses of monocot relationships: a summary. Aliso 22:63-75
17. Chaw SM, Parkinson CL, Cheng YC, Vincent TM, Palmer JD (2000) Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proc Natl Acad Sci USA 97:4086-4091
18. Covas G, Schnack B (1946) Numero de chromosomas en antofitas de la region de Cuya (Republica Argentina). Revista Argent Agron 13:152-166
19. Crandall-Stotler B, Stotler RE, Long DG (2009) Morphology and classification of the Marchantiophyta. In: Goffinet B, Shaw AJ (eds) Bryophyte biology, 2nd edn. Cambridge University Press, Cambridge, pp 1-54
20. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE et al. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16:738-749
21. Delevoryas T (1980) Polyploidy in gymnosperms. In: Lewis WH (ed) Polyploidy. Plenum Press, New York, pp 215-218
22. Dunlop DW (1949) Notes on the cytology of some lycopsids. Bull Torrey Bot Club 76:266-277
23. Elsik CG, Williams CG (2000) Retroelements contribute to the excess low-copy-number DNA in pine. Mol Gen Genet 264:47-55
24. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucl Acid Res 20:3639-3644
25. Gao L, Su YJ, Wang T (2010) Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. J Syst Evol 48:77-93
26. Greilhuber J, Leitch IJ (2013) Genome size and the phenotype. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 323-344
27. Greilhuber J, Sastad SM, Flatberg KI (2003) Ploidy determination in Sphagnum samples from Svalbard, Arctic Norway, by DNA image cytometry. J Bryol 25:235-239
28. Greilhuber J, Doležel J, Lysák MA, Bennett MD (2005) The origin, evolution and proposed stabilization of the terms ‘genome size’ and ‘C-value’ to describe nuclear DNA contents. Ann Bot 95:255-260
29. Greilhuber J, Borsch T, Müller K, Worberg A, Porembski S, Barthlott W (2006) Smallest angiosperm genomes found in Lentibulariaceae with chromosomes of bacterial size. Plant Biol 8:770-777
30. Grover C, Wendel JF (2010) Recent insights into mechanisms of genome size change in plants. J Bot Article ID 382732, 8 pp. doi:10.1115/2010/382732
31. Guillon JM (2004) Phylogeny of horsetails (Equisetum) based on the chloroplast rps4 gene and adjacent noncoding sequences. Syst Bot 29:251-259
32. Guillon JM (2007) Molecular phylogeny of horsetails (Equisetum) including chloroplast atpB sequences. J Plant Res 120:569-574
33. Hanson L, Leitch IJ (2002) DNA amounts for five pteridophyte species fill phylogenetic gaps in C-value data. Bot J Linn Soc 140:169-173
34. Hanson L, McMahon KA, Johnson MAT, Bennett MD (2001) First nuclear DNA C-values for 25 angiosperm families. Ann Bot 87:251-258
35. Ickert-Bond SM (2003) Systematics of new world Ephedra L. (Ephedraceae): integrating morphological and molecular data. Ph. D. thesis, Arizona State University
36. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
37. Jermy AC (1967) Cytomorphological variation in Selaginella. Bot J Linn Soc 60:147-158
38. Kejnovsky E, Leitch IJ, Leitch AR (2009) Contrasting evolutionary dynamics between angiosperm and mammalian genomes. Trends Ecol Evol 24:572-582
39. Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389:33-39
40. Khandelwal S (1990) Chromosome evolution in the genus Ophioglossum L. Bot J Linn Soc 102:205-217
41. Kuta E, Przywara L (2000) Cytotaxonomy of bryophytes in the Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Kraców, Poland. IOPB Newsl 32:3-8
42. Lang D, Zimmer AD, Rensing SA, Reski R (2008) Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends Plant Sci 13:542-549
43. Large MF, Braggins JE (1989) An assessment of characters of taxonomic significance in the genus Pilularia (Marsileaceae): with particular reference to P. americana, P. novae-follandiae, and P. novae-zelandiae. New Zealand J Bot 27:481-486
44. Leitch IJ, Bennett MD (2004) Genome downsizing in polyploid plants. Biol J Linn Soc 82:651-663
45. Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320:481-483
46. Leitch AR, Leitch IJ. (2012) Ecolgoical and genetic factors cause contrasting genome dynamics in seed plants.NewPhytol 194:629-646
47. Leitch IJ, Chase MW, Bennett MD (1998) Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Ann Bot 82(Suppl A):85-94
48. Leitch IJ, Soltis DE, Soltis PS, Bennett MD (2005) Evolution of DNA amounts across land plants (Embryophyta). Ann Bot 95:207-217
49. Leitch IJ, Beaulieu JM, Chase MW, Leitch AR, Fay MF (2010) Genome size dynamics and evolution in monocots. J Bot Article ID 862516, 18 pp. doi:10.1155/2010/862516
50. Lesho CL (1994) A summary of chromosome numbers in the Marsileaceae, with counts for additional species of Marsilea. Am Fern J 84:121-125
51. Loyal DS (1962) Abnormal sporelings of Regnellidium diphyllum Lindm. and chromosome number of the genus. Res Bull (NS) Panjab Univ 13:25-30
52. Manton I (1950) Problems of cytology and evolution in the Pteridophyta. Cambridge University Press, Cambridge
53. Marchant CJ (1968) Chromosome patterns and nuclear phenomena in the cycad families Stangeriaceae and Zamiaceae. Chromosoma 24:100-134
54. Martin NJ (1983)NuclearDNAvariation in the Australasian Loranthaceae. In: Calder M, Berhnhardt P (eds) Biology of mistletoes. Academic, Sydney, pp 277-293
55. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR et al (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101:14349-14354
56. Mishler BD, Kelch DG (2009) Phylogenomics and early land plant evolution. In: Goffinet B, Shaw AJ (eds) Bryophyte biology, 2nd edn. Cambridge University Press, Cambridge, pp 175-197
57. Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z et al (2009) Evolution of genome size and complexity in Pinus. PLoS One 4:e4332
58. Murray B (2013) Karyotype variation and evolution in gymnosperms. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 231-243
59. Nagalingum NS, Nowak MD, PryerKM (2008) Assessing phylogenetic relationships in extant heterosporous ferns (Salviniales), with a focus on Pilularia and Salvinia. Bot J Linn Soc 157:673-685
60. Nakazato T, Jung MK, Housworth EA, Rieseberg LH, Gastony GJ (2006) Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii. Genetics 173:1585-1597
61. Nakazato T, Barker MS, Rieseberg LH, Gastony GL (2008) Evolution of the nuclear genome of ferns and lycophytes. In: Ranker TA, Haufler CH (eds) Biology and evolution of ferns and lycophytes. Cambridge University Press, Cambridge, UK, pp 175-198
62. Newton ME (1985) Heterochromatin diversity in two species of Pellia (Hepaticae) as revealed by C-, Q-, N-and Hoechst 33258-banding. Chromosoma 92:378-386
63. Newton ME (1987) Developmental aspects of chromatin condensation in liverworts. Bryologist 90:376-382
64. Nickrent DL, Malécot V, Vidal-Russell R, Der JP (2010) A revised classification of Santalales. Taxon 59:538-558
65. Ogur M, Erickson RO, Rosen GU, Sax KB, Holden C (1951) Nucleic acids in relation to cell division in Lilium longiflorum. Exp Cell Res 2:73-89
66. Orzechowska M, Siwinska D, Maluszynska J (2010) Molecular cytogenetic analyses of haploid and allopolyploid Pellia species. J Bryol 32:113-121
67. Palmer JD, Soltis DE, Chase MW (2004) The plant tree of life: an overview and some points of view. Am J Bot 91:1437-1445
68. Parchman T, Geist K, Grahnen J, Benkman C, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180
69. Paton AJ, Brummitt N, Govaerts R, Harman K, Hinchcliffe S, Allkin B, Lughadha EN (2008) Towards target 1 of the global strategy for plant conservation: a working list of all known plant species - progress and prospects. Taxon 57:602-611
70. Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc 164:10-15
71. Pena MJ, Darvill AG, Eberhard S, York WS, O’Neill MA (2008) Moss and liverwort xyloglucans contain galacturonic acid and are structurally distinct from the xyloglucans synthesized by hornworts and vascular plants. Glycobiology 18:891-904
72. Peruzzi L, Cesca G, Puntillo D (2003) Isoetes (Isoetaceae), Ophioglossum and Botrychium (Ophioglossaceae) in Calabria (S Italy): more karyological and taxonomical data. Caryologia 56:359-363
73. Pichersky E, Soltis D, Soltis P (1990) Defective chlorophyll a/bbinding protein genes in the genome of a homosporous fern. Proc Natl Acad Sci USA 87:195-199
74. Proskauer J (1950) Notes on Hepaticae. I. Bryologist 53:166-172
75. Proskauer J (1958) Studies on the Anthocerotales. V. Phytomorphology 7:113-135
76. Proskauer J (1967) The variable ploidy life history of a monoecious self-fertilizing hornwort (Anthercerotales). Am J Bot 54:641-642
77. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD (2001) Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622
78. Przywara L, Kuta E (1995) Karyology of bryophytes. Pol Bot Stud 9:1-83
79. Qiu YL (2008) Phylogeny and evolution of charophytic algae and land plants. J Syst Evol 46:287-306
80. Qiu YL, Li LB, Wang B, Chen ZD, Knoop V et al (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 103:15511-15516
81. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64-69
82. Rensing SA, Beike AK, Lang D (2013) Evolutionary importance of generative polyploidy for genome evolution of haploid-dominant land plants. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 295-305
83. Renzaglia KS, Rasch EM, Pike LM (1995) Estimates of nuclear DNA content in bryophyte sperm cells: phylogenetic considerations. Am J Bot 82:18-25
84. Sax K, Beal JM (1934) Chromosomes of the Cycadales. J Arnold Arbor 15:255-258
85. Schneider H, Smith AR, Pryer KM (2009) Is morphology really at odds with molecules in estimating fern phylogeny? Syst Bot 34:455-475
86. Schuettpelz E, Pryer KM (2008) Fern phylogeny. In: Ranker TA, Haufler CH (eds) Biology and evolution of ferns and lycophytes. Cambridge University Press, Cambridge, pp 395-416
87. Shaw J, Renzaglia K (2004) Phylogeny and diversification of bryophytes. Am J Bot 91:1557-1581
88. Soltis PS, Soltis DE (2013) Angiosperm phylogeny: A framework for studies of genome evolution. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 1-11
89. Soltis DE, Soltis PS, Bennett MD, Leitch IJ (2003) Evolution of genome size in the angiosperms. Am J Bot 90:1596-1603
90. Soltis DE, Bell CD, Kim S, Soltis PS (2008) Origin and early evolution of angiosperms. Ann N Y Acad Sci 1133:3-25
91. Stergianou KK, Fowler K (1990) Chromosome numbers and taxonomic implications in the fern genus Azolla (Azollaceae). Plant Syst Evol 173:223-239
92. Takamiya M (1993) Comparative karyomorphology and interrelationships of Selaginella in Japan. J Plant Res 106:149-166
93. Tatuno S, Takei M (1969) Cytological studies of Salviniaceae I. Karyotype of two species in the genus Salvinia. Bot Magazine 82:403-408
94. Temsch EM, Greilhuber J, Krisai R (1998) Genome size in Sphagnum (peat moss). Bot Acta 111:325-330
95. Temsch EM, Greilhuber J, Krisai R (2010) Genome size in liverworts. Preslia 82:63-80
96. Tindale MD, Roy SK (2002) A cytotaxonomic survey of the Pteridophyta of Australia. Aust Syst Bot 15:839-937
97. Troìa A (2001) The genus Isoëtes L. (Lycophyta, Isoëtaceae): synthesis of karyological data. Webbia 56:201-218
98. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604
99. Vitte C, Bennetzen JL (2006) Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution. Proc Natl Acad Sci USA 103:17638-17643
100. Vitte C, Panaud O (2003) Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol Biol Evol 20:528-540
101. Voglmayr H (2000) Nuclear DNA amounts in mosses (Musci). Ann Bot 85:531-546
102. Voytas DF, Cummings MP, Konieczny A, Ausubel FM, Rodermel SR (1992) Copia-like retrotransposons are ubiquitous among plants. Proc Natl Acad Sci USA 89:7124-7128
103. Wang XY, Shi XL, Hao BL, Ge S, Luo JC (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165:937-946
104. Weiss-Schneeweiss H, Schneeweiss GM (2013) Karyotype diversity and evolutionary trends in angiosperms. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 209-230
105. Werner T, Braukmann TWA, Kuzmina M, Stefanovic S (2009) Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Curr Genet 55:323-337
106. Wiens D (1964) Chromosome numbers in North American Loranthaceae: (Arceuthobium, Phoradendron, Psittacanthus, Struthanthus). Am J Bot 51:1-6
107. Wiens D (1968) Chromosomal and flowering characteristics in dwarf mistletoes (Arceuthobium). Am J Bot 55:325-334
108. Wiens D, Barlow BA (1971) The cytogeography and relationships of the viscaceous and eremolepidaceous mistletoes. Taxon 20:313-332
109. Zheng M, Zhu R-L (2009) Karyological studies on some liverworts from China and Singapore. Fieldiana Bot 81:87
110. Zonneveld BJM (2010) New record holders for maximum genome size in eudicots and monocots. J Bot. doi:10.1155/2010/527357, Article ID 527357