Karyotype variation and evolution in gymnosperms

Plant Genome Diversity

Volumn 2, Issue , 2013, Pages 231-243

  Murray, Brian G ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84930744610     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1160-4_14     Document Type: Chapter

References (117)

1. Barker MS, Graham SW, Rieseberg LH (2010) Comparative gymnosperm transcriptomics. Abstract for Botany 2010 meeting, USA. http://2010.botanyconference.org/engine/search/index.php? func=detail&aid=437, Accessed on 18 June 2011
2. Bogunic F, Muratovic E, Siljak-Yakovlev S (2006) Chromosomal differentiation between Pinus heldreichii and Pinus nigra. Ann For Sci 63:267-274
3. 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
4. Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics 6:143
5. Brown GR, Carlson JE (1997) Molecular cytogenetics of the genes encoding 18S-5.8S-26S rRNA and 5S rRNA in two species of spruce (Picea). Theor Appl Genet 95:1-9
6. Brown GR, Amarasinghe V, Kiss G, Carlson JE (1993) Preliminary karyotype and chromosomal location of ribosomal DNA in white spruce using fluorescence in situ hybridization. Genome 36:310-316
7. Brown GR, Newton CH, Carlson JE (1998) Organization and distribution of a Sau3A tandem repeated DNA sequence in Picea (Pinaceae) species. Genome 41:560-565
8. Cafasso D, Cozzolino S, Chinali G, De Luca P (2003) An unusual satellite DNA from Zamia paucijuga (Cycadales) characterized by two different organizations of the repetitive unit in the plant genome. Gene 311:69-77
9. Cafasso D, Cozzolino S, Vereecken NJ, De Luca P, Chinali G (2009) Organization of a dispersed repeated DNA element in the Zamia genome. Biol Plant 53:28-36
10. Caputo P, Cozzolino S, Gaudio L, Moretti A, Stevenson DW (1996) Karyology and phylogeny of some Mesoamerican species of Zamia (Zamiaceae). Am J Bot 83:1513-1520
11. Chase MW, Reveal JL (2009) A phylogenetic classification to accompany APG III. Bot J Linn Soc 161:122-127
12. 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
13. Chaw S-M, Walters TW, Chang C-C, Hu S-H, Chen S-H (2005) A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Mol Phylogenet Evol 37:214-234
14. Chuang T-I, Hu WWL (1963) Study of Amentotaxus argotaenia (Hance) Pilger. Bot Bull Acad Sin 4:10-14
15. Chumley TW, McCoy SKR, Raubeson LA (2008) Gne-deep: exploring Gnetalean affinities in seed plant phylogeny with 83 plastid genes. Abstract for Botany 2008meeting, USA.http://2008.botanyconference. org/engine/search/index.php?func=detail&aid=770
16. 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
17. Datson PM, Murray BG (2006) Ribosomal DNA locus evolution in Nemesia: transposition rather than structural rearrangement as the key mechanism? Chromosome Res 14:845-867
18. Davies BJ, O'Brien IEW, Murray BG (1997) Karyotypes, chromosome bands and genome size variation in New Zealand endemic gymnosperms. Plant Syst Evol 208:169-185
19. Doudrick RL, Heslop-Harrison JS, Nelson CD, Schmidt T, Nance WL, Schwarzacher T (1995) Karyotype of slash pine (Pinus elliottii var. elliottii) using patterns of fluorescence in situ hybridization and fluorochrome banding. J Hered 86:289-296
20. Eckenwalder JE (2009) Conifers of the world. Timber Press, Portland
21. Elsik CG, Williams CG (2000) Retroelements contribute to the excess low-copy-number DNA in pine. Mol Gen Genet 264:47-55
22. Fawcett JA, Van de Peer Y, Maere S (2013) Significance and biological consequences of polyploidization in 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 277-293
23. Friesen N, Brandes A, Heslop-Harrison JS (2001) Diversity, origin and distribution of retrotransposons (gypsy and copia) in conifers. Mol Biol Evol 18:1176-1188
24. Fuchs J, Brandes A, Schubert I (1995) Telomere sequence localization and karyotype evolution in higher plants. Plant Syst Evol 196:227-241
25. Garcia S, Garnatje T, Hidalgo O, McArthur ED, Siljak-Yakovlev S, Vallès J (2007) Extensive ribosomal DNA (18S-5.8S-26S and 5S) colocalization in the North American endemic sagebushes (subgenus tridentatae, Artimisia, Asteraceae) revealed by FISH. Plant Syst Evol 267:79-92
26. Givnish TJ (1980) Ecological constraints on the evolution of breeding systems in seed plants: dioecy and dispersal in gymnosperms. Evolution 34:959-972
27. Grover C, Wendel JF (2010) Recent insights into mechanisms of genome size change in plants. J Bot 2010:1-8 Article ID 382732
28. Guan Q-L, Yu Z-L, Feng Y-L (1993) Studies of chromosomes in Amentotaxus argotaenia. Acta Bot Yunnan 15:385-391
29. Hizume M (1988) Karyomorphological studies in the family Pinaceae. Mem Fac Educ Ehime Univ Nat Sci 8:1-108
30. Hizume M (1995) Physical mapping of 5S rRNA genes in Cycas revoluta. Cytologia 60:389-393
31. HizumeM(1997) Chromosomes of Ginkgo biloba. In: Hori T et al. (eds) Ginkgo biloba-A global treasure. Springer, Tokyo, pp 109-118
32. Hizume M, AkiyamaM(1992) Size variation of chromomycin A3-band in chromosomes of Douglas fir, Pseudotsuga menziesii. Jpn J Genet 67:425-435
33. Hizume M, Kuzukawa Y (1995) Fluorescent chromosome banding in Picea II. Relationships between rDNA loci and chromomycin A3-bands in somatic chromosomes of Picea jezoensis var. hondoensis. La Kromosomo II 79-80:2754-2759
34. Hizume M, Tanaka A (1990) Fluorescent chromosome bandings in two American larches, Larix occidentalis and L. laricina. LaKromosomo II 58:1979-1987
35. Hizume M, Abe KK, Tanaka A (1988a) Fluorescent chromosome banding in the Taxodiaceae. La Kromosomo II 50:1609-1619
36. Hizume M, Shiraishi H, Tanaka A (1988b) A cytological study of Podocarpus macrophyllus with special reference to sex chromosomes. Jpn J Genet 63:413-423
37. Hizume M, Kishimoto K, Kubo Y, Tanaka A (1989) Fluorescent chromosome banding in Picea I. Differences in chromomycin A3 band pattern between P. jesoensis var. jesoensis and P. jesoensis var. hondoensis. La Kromosomo II 53:1736-1744
38. Hizume M, Kitazawa N, Gu Z, Kondo K (1991) Variation of fluorescent chromosome band in Picea brachytyla var. complanata collected in Yunnan, China. La Kromosomo II 63-64:2149-2158
39. Hizume M, Ishida F, MurataM(1992a) Multiple locations of the rRNA genes in chromosomes of pines, Pinus densiflora and P. thunbergii. Jpn J Genet 67:389-396
40. Hizume M, Ishida F, Kondo K (1992b) Differential staining and in situ hybridization of nucleolar organizers and centromeres in Cycas revoluta chromosomes. Jpn J Genet 67:381-387
41. Hizume M, Tominaga HH, Kondo K, Gu Z, Yue Z (1993) Fluorescent chromosome banding in six taxa of Eurasian Larix, Pinaceae. La Kromosomo II 69:2342-2354
42. Hizume M, Kuzukawa Y, Kondo T, Yang Q, Hong D, Tanaka R (1995) Localization of rDNA and fluorescent bandings in chromosomes of Larix potaninii var. macrocarpa collected in Sichuan, China. La Kromosomo II 78:2689-2694
43. Hizume M, Kuzukawa Y, Kondo T (1996) Physical mapping of 5S rDNA locus on chromosomes in Pseudotsuga menziesii, Pinaceae. La Kromosomo II 83-84:2901-2908
44. Hizume M, Kurose N, Shibata F, Kondo K (1998a) Molecular cytogenetic studies on sex chromosomes and proximal heterochromatin containing telomere-like sequences in Cycas revoluta. Chromosome Sci 2:63-72
45. Hizume M, Shibata F, Kondo T (1998b) Fluorescence in situ hybridization of ribosomal RNA gene in Cryptomeria japonica, Taxodiaceae. Chromosome Sci 2:99-102
46. Hizume M, Shibata F, Kondo K, Hoshi Y, Kondo T, Ge S, Yang Q, Hong D (1999) Identification of chromosomes in two Chinese spruce species by multicolour fluorescence in situ hybridization. Chromosome Sci 3:37-41
47. Hizume M, Shibata F, Matsusaki Y, Kondo K (2000) Chromosomal localization of telomere sequence repeats in five gymnosperm species. Chromosome Sci 4:39-42
48. Hizume M, Shibata F, Maruyama Y, Kondo T (2001) Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. Zucc Chromosoma 110:345-351
49. Hizume M, Shibata F, Matsusaki Y, Garajova Z (2002a) Chromosome identification and comparative karyotypic analyses of Pinus species. Theor Appl Genet 105:491-497
50. Hizume M, Shibata F, Matsumoto A, Maruyama Y, Hayashi E, Kondo T, Kondo K, Zhang S, Hong D (2002b) Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae. Genome 45:777-783
51. Houben A, Moghaddam AMB, Klemme S (2013) Biology and evolution of B chromosomes. 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 149-165
52. Ickert-Bond SM (2003) Systematics of New World Ephedra L. (Ephedraceae): integrating morphological and molecular data. Thesis, Arizona State University, pp 363
53. Islam-Faridi MN, Nelson CD, Kubisiak TL (2007) Reference karyotype and cytomolecular map for loblolly pine (Pinus taeda L.). Genome 50:241-251
54. Jacobs MD, Gardner RC, Murray BG (2000) Cytological characterization of heterochromatin and rDNA in Pinus radiata and P. taeda. Plant Syst Evol 223:71-79
55. Janoušek B, Hobza R, Vyskot B (2013) Chromosomes and sex diffrentiation. 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 167-186
56. Kamm A, Doudrick RL, Heslop-Harrison JS, Schmidt T (1996) The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc Natl Acad Sci USA 93:2708-2713
57. Khoshoo TN (1959) Polyploidy in gymnosperms. Evolution 13:24-39
58. Khoshoo TN, Ahuja MR (1963) The chromosomes and relationships of Welwitschia mirabilis. Chromosoma 14:522-533
59. Kokubugata G, Kondo K (1994) Quantitative variability in karyotype of Cycas revoluta. La Kromosomo II 75-76:2613-2618
60. Kokubugata G, Kondo K (1996) Differential fluorescent-banding patterns in chromosomes of four species of Cycas (Cycadaceae). Bot J Linn Soc 120:51-55
61. Kokubugata G, Kondo K (1998) Comparative karyotype analysis of Ceratozamia mexicana and Microcycas calocoma (Zamiaceae) using fluorochrome banding (CMA/DAPI) and fluorescence in situ hybridization of ribosomal DNA. Plant Syst Evol 210:41-50
62. Kokubugata G, Kondo K, Randall LM (1999) Comparison of chromosome number and karyotype of two Lepidozamia species (Zamiaceae, Cycadales). Ann Tsukuba Bot Gard 18:65-69
63. Kokubugata G, Kondo K, Wilson GW, Randall LM, van der Schans A, Morris DK (2000) Comparison of karyotype and rDNA-distribution in somatic chromosomes of Bowenia species (Stangeriaceae, Cycadales). Austral Syst Bot 13:15-20
64. Kokubugata G, Hill KD, Kondo K (2002) Ribosomal DNA distribution in somatic chromosomes of Stangeria eriopus (Stangeriaceae, Cycadales) and molecular-cytotaxonomic relationships to some other cycad genera. Brittonia 54:1-5
65. Kokubugata G, Vovides AP, Kondo K (2004) Mapping 5S ribosomal DNA on somatic chromosomes of four species of Ceratozamia and Stangeria eriopus (Cycadales). Bot J Linn Soc 145:499-504
66. Kriebel HB (1985) DNA sequence components of the Pinus strobus genome. Can J For Res 15:1-4
67. Krutovsky KV, Troggio M, Brown GR, Jermstad KD, Neale DB (2004) Comparative mapping in the Pinaceae. Genetics 168:447-461
68. Kupila-Ahvenniemi S, Hohtola A (1977) Structure of the chromosomes of Scotch pine. Hereditas 87:185-188
69. Kurdi-Haidar B, Shalhoub V, Dib-Haji S, Deeb S (1983) DNA sequence organization in the genome of Cycas revoluta. Chromosoma 88:319-327
70. Leitch AR, Leitch IJ (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol 194:629-646
71. Leitch IJ, Leitch AR (2013) Genome size diversity and evolution in 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 307-322
72. Leitch IJ, Hanson L, Winfield M, Parker J, Bennett MD (2001) Nuclear DNA C-values complete familial representation in gymnosperms. Ann Bot 88:843-849
73. Liu Z-L, Zhang D, Hong D-Y, Wang X-R (2003) Chromosomal localization of 5S and 18S-5.8S-25S ribosomal DNA sites in five Asian pines using fluorescence in situ hybridization. Theor Appl Genet 106:198-204
74. Lubaretz O, Fuchs J, Ahne R, Meister A (1996) Karyotyping of three Pinaceae species via fluorescent in situ hybridization and computeraided chromosome analysis. Theor Appl Genet 92:411-416
75. MacPherson P, Filion WG (1981) Karyotype analysis and the distribution of constitutive heterochromatin in five species of Pinus. J Hered 72:193-198
76. Marchant CJ (1968) Chromosome patterns and nuclear phenomena in the cycad families Stangeriaceae and Zamiaceae. Chromosoma 24:100-134
77. Matthey R (1945) L'évolution de la formule chromosomiale chez les Vertébrés. Experientia 1(50-56):78-86
78. Miksche JP, Hotta Y (1973) DNA base composition and repetitious DNA in several conifers. Chromosoma 41:29-36
79. Miller CI (1993) Impact of the Eocene on the evolution of Pinus L. Ann Missouri Bot Gard 80:471-498
80. Moretti A (1990) Cytotaxonomy of cycads. Mem NY Bot Gard 57:114-122
81. Morse AM, Peterson DG, Islam-Faridi MN, Smith KE, Magbanua Z, Garcia SA, Kubisiak TL, Amerson HV, Carlson JE, Nelson CD, Davis JM (2009) Evolution of genome size and complexity in Pinus. PLoS One 4:e4332
82. Murray BG (1998) Nuclear DNA amounts in gymnosperms. Ann Bot 82(Suppl A):3-15
83. Murray BG, Friesen N, Heslop-Harrison JS (2002) Molecular cytogenetic analysis of Podocarpus and comparison with other gymnosperm species. Ann Bot 89:483-489
84. Murray BG, Leitch IJ, Bennett MD (2010) Gymnosperm DNA C-values database (release 4.0, Dec 2010). http://data.kew.org/cvalues/
85. Page CN (1990) Gymnosperms. In: Kramer KU, Green PS (eds) The families and genera of vascular plants. Springer, Berlin, pp 280-361
86. 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
87. 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
88. Pellicer J, Fay MF, Leitch IJ (2010) The largest eukaryotic genome of them all? Bot J Linn Soc 164:10-15
89. Puizina J, Sviben T, Krajacic-Sokol I, Zoldos-Pecnik V, Siljak-Yakovlev S, Papes D (2008) Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae. Plant Biol 10:256-267
90. Quinn CJ, Rattenbury JA (1972) Structural hybridity in New Zealand Dacrydium. New Zealand J Bot 10:427-436
91. Rai HS, Reeves PA, Peakall R, Olmstead RG, Graham SW (2008) Inference of higher-order conifer relationships from a multi-locus plastid data set. Botany 86:658-669
92. Rake AV, Miksche JP, Hall RB, Hansen KM (1980) DNA reassociation kinetics of four conifers. Can J Genet Cytol 22:69-79
93. Sangduen N, Toahsakul M, Hongtrakul V (2009) Comparative karyomorphological study between male and female plants of some Cycas and Zamia species. Kasetsart J (Nat Sci) 43:476-485
94. Sax HJ (1932) Chromosome pairing in Larix species. J Arnold Arb 13:368-373
95. Sax K (1960) Meiosis in interspecific pine hybrids. Forest Sci 6:135-138
96. Saylor LC, Smith BW (1966) Meiotic irregularity in species and interspecific hybrids of Pinus. Am J Bot 53:453-468
97. Schmidt A, Doudrick RL, Heslop-Harrison JS, Schmidt T (2000) The contribution of short repeats of low sequence complexity to large conifer genomes. Theor Appl Genet 101:7-14
98. Segawa M, Kishi S, Tatsuno S (1971) Sex chromosomes of Cycas revoluta. Jpn J Genet 46:33-39
99. Shibata F, Hizume M, Garajova Z (2004) Conserved FISH karyotypes in four species of Abies (Pinaceae). Chromosome Sci 8:95-98
100. Shibata F,Matsusaki Y, HizumeM(2005) AT-rich sequences containing Arabidopsis-type telomere sequence and their chromosomal distribution in Pinus densiflora. Theor Appl Genet 110:1253-1258
101. Siljak-Yakovlev S, Cerbah M, Coulaud J, Stoian V, Brown SC, Zoldos V, Jelenic S, Papes D (2002) Nuclear DNA content, base composition, heterochromatin and rDNA in Picea omorika and Picea abies. Theor Appl Genet 104:505-512
102. Sone T, Fujisawa M, Takenaka M, Nakagawa S, Yamaoka S, Sakaida M, Nishiyama R, Yamato KT, Ohimodo N, Fukui K, Fukuzawa H, Ohyama K (1999) Bryophyte 5S rDNA was inserted into 45S rDNA repeat units after the divergence from higher land plants. Plant Mol Biol 41:679-685
103. Stockey RA, NishidaM(1986) Pinus harborensis sp. nov. and affinities of permineralized leaves from the Upper Cretaceous of Japan. Can J Bot 64:1856-1866
104. Tagashira N, Kondo K (1999) A karyotype comparison of nine species of aneuploid Zamia by using the conventional orcein staining and the fluorochrome CMA-DAPI differential staining methods. Cytologia 64:449-458
105. Tagashira N, Kondo K (2001) Chromosome phylogeny of Zamia and Ceratozamia by means of Robertsonian changes detected by fluorescence in situ hybridization (FISH) technique of rDNA. Plant Syst Evol 227:145-155
106. Tanaka R, Hizume M(1980) C banding treatment for the chromosomes of some gymnosperms. Bot Mag Tokyo 93:167-170
107. Teoh SB, Rees H (1977) B chromosomes in white spruce. P Roy Soc Lond B Bio 198:325-344
108. Trivers R, Burt A, Palestris BG (2004) B chromosomes and genome size in flowering plants. Genome 47:1-8
109. Vovides AP, Olivares M (1996) Karyotype polymorphism in the cycad Zamia loddigesii (Zamiaceae) of the Yucatan Peninsula, Mexico. Bot J Linn Soc 120:77-83
110. Wardle P (1972) Podocarpus totara var. waihoensis var. nov.: The result of introgressive hybridization between P. totara and P. acutifolius. New Zealand J Bot 10:195-201
111. 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
112. 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
113. White MJD (1973) Animal cytology and evolution. Cambridge University Press, Cambridge
114. Williams CG (2009) Conifer reproductive biology. Springer, Dordrecht
115. Williams CG, Joyner KL, Auckland LD, Johnston S, Price HJ (2002) Genomic consequences of Pinus spp. hybridization. Biol J Linn Soc 75:503-508
116. Zgurski JM, Rai HS, Fai QM, Bogler DJ, Francisco-Ortega J, Graham SW (2008) How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set. Mol Phylogenet Evol 47:1232-1237
117. Zhou Q-x, Z-j Gu, Yue Z-S (2000) Karyomorphology and relationships of Amentotaxus Pilg. Acta Phytotax Sin 36:522-527