Incongruent patterns of local and global genome size evolution in cotton

Genome Research

Volumn 14, Issue 8, 2004, Pages 1474-1482

  Grover, Corrinne E ^a   Kim, HyeRan ^b   Wing, Rod A ^b   Paterson, Andrew H ^c   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULOSE SYNTHASE; DNA; DNA FRAGMENT; SPACER DNA; SYNTHETASE; UNCLASSIFIED DRUG;

ALLOPOLYPLOIDY; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTROLLED STUDY; COTTON; DNA CONTENT; GENE NUMBER; GENE ORDER; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENOME SIZE; GENOMIC ISLAND; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYPLOIDY; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE HOMOLOGY; SPECIES DIFFERENTIATION; TRANSPOSON;

BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; GOSSYPIUM; MOLECULAR SEQUENCE DATA; PHYLOGENY; PHYSICAL CHROMOSOME MAPPING; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

GOSSYPIUM; GOSSYPIUM HIRSUTUM; MYA;

EID: 4444262329     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2673204     Document Type: Article

References (96)

1. Adams, K.L. and Palmer, J.D. 2003. Evolution of mitochondrial gene content: Gene loss and transfer to the nucleus. Mol. Phylogenet. Evol. 29: 380-395.
2. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant, Arabidopsis thaliana. Nature 408: 796-815.
3. Bennett, M.D. 1985. Intraspecific variation in DNA amount and the nucleotypic dimension in plant genetics. In Plantgenetics (ed. M. Freeling), pp. 283-302. A.R. Liss, New York.
4. Bennet, M.D. 1987. Variation in genomic form and its ecological implications. New Phytol. 106: 177-200.
5. Bennett, M.D. and Leitch, I.J. 1995. Nuclear DNA amounts in angiosperms. Annals Bot. 76: 113-176.
6. Bennett, M.D. and Leitch, I.J. 1997. Nuclear DNA amount in angiosperms. Phil. Trans. Royal Soc. London B 334: 309-345.
7. Bennett, M.D. and Leitch, I.J. 2003. Plant DNA C-values database. http://www.rbgkew.org.uk/cval/homepage.html.
8. Bennetzen, J.L. 2000a. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
9. Bennetzen, J.L. 2000b. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
10. Bennetzen, J.L. 2002. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36.
11. Bennetzen, J.L. and Kellogg, E.A. 1997. Do plants have a one-way ticket to genomic obesity? Plant Cell 9: 1509-1514.
12. Bensasson, D., Petrov, D.A., Zhang, D.X., Hartl, D.L., and Hewitt, G.M. 2001. Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol. Biol. Evol. 18: 246-253.
13. Bertran, E. and Long, M. 2002. Expansion of genome coding region by acquisition of new genes. Genetica 115: 65-80.
14. Biderre, C., Metenier, G., and Vivares, C.P. 1998. A small spliceosomal-type intron occurs in a ribosomal protein gene of the microsporidian Encephalitozoon cuniculi. Mol. Biochem. Parasitol. 74: 229-231.
15. Brudno, M., Do, C., Cooper, G., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003. LAGAN and Multi-LAGAN: Efficient tools for large scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
16. Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268: 78-94.
17. Cavalier-Smith, T. 1985. The evolution of genome size. John Wiley, New York.
18. Chantret, N., Cenci, A., Sabot, F., Anderson, O., and Dubcovsky, J. 2004. Sequencing of the Triticum monococcum Hardness locus reveals good microcolinearity with rice. Mol. Genet. Genom. Online First: 1617-4623.
19. Chen, M., SanMiguel, P., de Oliveira, A.C., Woo, S.-S., Zhang, H., Wing, R.A., and Bennetzen, J.L. 1997. Microcolinearity in sh2-homoeologous regions of the maize, rice, and sorghum genomes. Proc. Natl. Acad. Sci. 94: 3431-3435.
20. Chen, M.S., SanMiguel, P., and Bennetzen, J.L. 1998. Sequence organization and conservation in sh2/a1-homoeologous regions of sorghum and rice. Genetics 148: 435-443.
21. Chooi, W.Y. 1971. Variation in nuclear DNA content in the genus Vicia. Genetics 68: 195-211.
22. Claverie, J.-M. 2000. What if there are only 30,000 human genes? Science 291: 1255-1257.
23. Cronn, R.C., Small, R.L., Haselkorn, T., and Wendel, J.F. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Botany 89: 707-725.
24. Deutsch, M. and Long, M. 1999. Intron-exon structure of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
25. Devons, K.M., Brown, J.K.M., and Bennetzen, J.L. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079.
26. Dubcovsky, J., Ramakrishna, W., SanMiguel, P.J., Busso, C.S., Yan, L.L., Shiloff, B.A., and Bennetzen, J.L. 2001. Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiology 125: 1342-1353.
27. Endrizzi, J.D., Turcotte, E.L., and Kobel, R.J. 1985. Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23: 271-375.
28. Ewing, B. and Green, P. 1998. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
29. Ewing, B., Hillier, L., Wendl, M.C., and Green, P. 1998. Base-calling of automated sequences traces using phred. I. Accuracy assessment. Genome Res. 8: 175-185.
30. Feschotte, C. and Mouches, C. 2000. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a POGO-like DNA transposon. Mol. Biol. Evol. 17: 730-737.
31. Feschotte, C., Zhang, X., and Wessler, S.R. 2002. Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. In Mobile DNA II (ed. N.L. Craig). ASM Press, Washington, DC.
32. Fu, H.H. and Dooner, H.K. 2002. Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. 99: 9573-9578.
33. Gale, M.D. and Devos, K.M. 1998. Plant comparative genetics after 10 years. Science 282: 656-659.
34. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
35. Gordon, D., Abajian, C., and Green, P. 1998. CONSED: A graphical tool for sequence finishing. Genome Res. 8: 195-202.
36. Green, P. 1999. Phrap documentation. http://www.phrap.org/phrap.docs/phrap.html.
37. Gregory, T.R. 2001. Animal genome size database. http://www.genomesize.com.
38. Gregory, T.R. 2002. Genome size and developmental complexity. Genetica 115: 131-146.
39. Gregory, T.R. and Hebert, P.D.N. 1999. The modulation of DNA content: Proximate causes and ultimate consequences. Genome Res. 9: 317-324.
40. Ilic, K., SanMiguel, P.J., and Bennetzen, J.L. 2003. A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc. Natl. Acad. Sci. 100: 12265-12270.
41. Jones, R.N. and Brown, L.M. 1976. Chromosome evolution and DNA variation in Crepsis. Heredity 36: 91-104.
42. Jurka, J. 2000. Repbase Update: A database and an electronic journal of repetitive elements. Trends Genet. 9: 418-420.
43. Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. 1996. CENSOR - A program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20: 119-122.
44. Kalendar, R., Tanskanen, J., Immonen, S., New, E., and Schulman, A.H. 2000. Genome evolution in wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. 97: 6603-6607.
45. Kellis, M., Birren, B.W., and Lander, E. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428: 617-624.
46. Kirik, A., Salomon, S., and Puchta, H. 2000. Species-specific double-strand break repair and genome evolution in plants. EMBO J. 2000: 5562-5566.
47. Ku H.M., Vision, T., Liu, J., and Tanksley, S.D. 2000. Comparing sequenced segments of tomato and Arabidopsis genomes: Large scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. 97: 9121-9126.
48. Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A., and Freeling, M. 2004. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166: 935-945.
49. Langley, C.H., Montgomery, E., Hudson, R., Kaplan, N., and Charlesworth, B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. 52: 223-235.
50. Leitch, I.J., Chase, M.W., and Bennett, M.D. 1998. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Annals Bot. (Suppl. A) 82: 85-94.
51. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, MA.
52. Li, W.-H. and Graur, D. 1991. Fundamentals of molecular evolution. Sinauer Associates, Sunderland, MA.
53. Lukashin, A. and Borodovsky, M. 1998. GeneMark.hmm: New solutions for gene finding. Nucleic Acids Res. 26: 1107-1115.
54. Ma, J., Dews, K.M., and Bennetzen, J.L. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
55. McLysaght, A., Enright, A.J., Skrabanek, L., and Wolfe, K.H. 2000. Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human. Yeast 17: 22-36.
56. Mirsky A.E. and Ris, H. 1951. The DNA content 5 animal cells and its evolutionary significance. J. Gen. Physiol. 34: 451-462.
57. Moriyama, E.N., Petrov, D.A., and Hartl, D.L. 1998. Genome size and intron size in Drosophila. Mol. Biol. Evol. 15: 770-773.
58. Orel, N. and Puchta, H. 2003. Differences in the processing of DNA ends in Arabidopsis thaliana and tobacco: Possible implications for genome evolution. Plant Mol. Biol. 51: 523-531.
59. Petrov, D.A. 2001. Evolution of genome size: New approaches to an old problem. Trends Genet. 17: 23-28.
60. Petrov, D.A. 2002a. DNA loss and evolution of genome size in Drosophila. Genetica 115: 81-91.
61. Petrov, D.A. 2002b. Mutational equilibrium model of genome size evolution. Theoret. Pop. Biol. 61: 531-544.
62. Petrov, D.A. and Wendel, J.F. 2004. Evolution of eukaryotic genome structure. In Evolutionary genetics: Concepts and case studies (eds. C.W. Fox and J.B. Wolf). Oxford Univ. press, Oxford.
63. Petrov, D.A., Aminetzach, Y.T., Davis, J.C., Bensasson, D., and Hirsh, A.E. 2003. Size matters: Non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol. 20: 880-892.
64. Ramakrishna, W., Dubcovsky, J., Park, Y.J., Busso, C., Emberton, J., SanMiguel, P., and Bennetzen, J.L. 2002a. Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162: 1389-1400.
65. Ramakrishna, W., Emberton, J., Ogden, M., SanMiguel, P., and Bennetzen, J.L. 2002b. Structural analysis of the maize Rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14: 3213-3223.
66. Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569.
67. Rong, J., Abbey, C., Bowers, J.E., Brubaker, C.L., Chang, C., Chee, P.W., Delmonte, T.A., Ding, X., Garza, J.J., and Marler, B.S., 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166: 389-417.
68. Rossberg, M., Theres, K., Acarkan, A., Herrero, R., Schmitt, T., Schumacher, K., Schmitz, G., and Schmidt, R. 2001. Comparative sequence analysis reveals extensive microcolinearity in the Lateral suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13: 979-988.
69. SanMiguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z., et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
70. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y., and Bennetzen, J.L. 1998. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20: 43-45.
71. m. Funct. Integr. Genomics 2: 70-80.
72. Seelanan, T., Schnabel, A., and Wendel J.F. 1997. Congruence and consensus in the cotton tribe. Syst. Bot. 22: 259-290.
73. Senchina, D.S., Alvarez, I., Cronn, R.C., Liu, B., Rong, J.K., Noyes, R.D., Paterson, A.H., Wing, R.A., Wilkins, T.A., and Wendel, J.F. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20: 633-643.
74. Shahmuradov, I.A., Akbarova, Y.Y., Solovyev, V.V., and Aliyev, J.A. 2003. Abundance of plastid DNA insertions in nuclear genomes of rice and Arabidopsis. Plant Mol. Biol. 52: 923-934.
75. Shirasu, K., Schulman, A.H., Lahaye, T., and Schulze-Lefert, P. 2000. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908-915.
76. Small, R.L., Ryburn, J.A., Cronn, R.C., Seelanan, T., and Wendel, J.F. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. Am. J. Botany 85: 1301-1315.
77. Tarchini, R., Biddle, P., Wineland, R., Tingey, S., and Rafalski, A. 2000. The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381-391.
78. Thomas, C.A. 1971. The genetic organisation of chromosomes. Annu. Rev. Genet. 5: 237-256.
79. Tikhonov, A.P., SanMiguel, P.J., Nakajima, Y., Gorenstein, N.M., Bennetzen, J.L., and Avramova, Z. 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Natl. Acad. Sci. 96: 7409-7414.
80. Tomkins, J.P., Peterson, D.G., Yang, T.J., Main, D., Wilkins, T.A., Paterson, A.H., and Wing, R.A. 2001. Development of genomic resources for cotton (Gossypium hirsutum L.): BAC library construction, preliminary STC analysis, and identification of clones associated with fiber development. Mol. Breed. 8: 255-261.
81. Tu, Z. 2001. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. 98: 1699-1704.
82. Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., and Van de Peer, Y. 2002. The automatic detection of homoeologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12: 1792-1801.
83. van Leeuwen, H., Monfort, A., Zhang, H.B., and Puigdomenech, P. 2003. Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. Plant Mol. Biol. 51: 703-718.
84. Vicient, C.M., Suoniemi, A., Anamthawat-Jonsson, K., Tanskanen, J., Beharav, A., Nevo, E., and Schulman, A.H. 1999. Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769-1784.
85. Vinogradov, A.E. 1999. Intron-genome size relationship on a large evolutionary scale. J. Mol. Evol. 49: 376-384.
86. Vision, T.J., Brown, D.G., and Tanksley, S.D. 2000. The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
87. Vitte, C. and Panaud, O. 2003. Formation of solo-LTRs through unequal homoeologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Mol. Biol. Evol. 20: 528-540.
88. Wendel, J.F. 2000. Genome evolution in polyploids. Plant Mol. Biol. 42: 225-249.
89. Wendel, J.F. and Cronn, R.C. 2003. Polyploidy and the evolutionary history of cotton. Adv. Agron. 78: 139-186.
90. Wendel, J.F., Croon, R.C., Alvarez, I., Liu, B., Small, R.L., and Senchina, D.S. 2002a. Intron size and genome size in plants. Mol. Biol. Evol. 19: 2346-2352.
91. Wendel, J.F., Croon, R.C., Johnston, J.S., and Price, H.J. 2002b. Feast and famine in plant genomes. Genetica 115: 37-47.
92. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E., and Keller, B. 2001. Analysis of a continuous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26: 307-316.
93. m genomes of wheat. Plant Cell 15: 1186-1197.
94. Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
95. Zhang, J. 2003. Evolution by gene duplication: An update. Trends Ecol. Evol. 18: 292-298.
96. Zhao, X.P., Si, Y., Hanson, R.E., Crane, C.F., Price, H.J., Stelly, D.M., Wendel, J.F., and Paterson, A.H. 1998. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res. 8: 479-492.