The variation of base composition in plant genomes

Plant Genome Diversity Volume 1: Plant Genomes, their Residents, and their Evolutionary Dynamics

Volumn , Issue , 2012, Pages 209-235

  Šmarda, Petr ^a   Bureš, Petr ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84948079899     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1130-7_14     Document Type: Chapter

References (207)

1. Aird D, Chen WS, Ross M, Connolly K, Meldrim J, Russ C, Fisher S, Jaffe D, Nusbaum C, Gnirke A (2010) Analyzing and minimazing bias in Illumina sequencing libraries. Genome Biol 11(Suppl 1):P3
2. Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao SM et al (2003) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13:753-763
3. Alexandrov BV, Freidin S, Troukhan M, Tatarinova T, Zhang H, Swaller T, Lu Y, Bouck J, Flavell R et al (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69:179-194
4. Anselmi C, Bocchinfuso G, De Santis P, Savino M, Scipioni A (1999) Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J Mol Biol 286:1293-1301
5. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
6. Bai L, Morozov AV (2010) Gene regulation by nucleosome positioning. Trends Genet 26:476-483
7. Barow M, Meister A (2002) Lack of correlation between AT frequency and genome size in higher plants and the effect of nonrandomness of base sequences on dye binding. Cytometry 47:1-7
8. Barton LL (2005) Physiological basis for the growth in extreme environments. In: Barton L (ed) Structural and functional relationships in prokaryotes. Springer, Berlin/Heidelberg/New York, pp 348-393
9. Basak S, Mukhopadhyay P, Gupta SK, Ghosh TC (2010) Genomic adaptation of prokaryotic organisms at high temperature. Bioinformation 4:352-356
10. Bennett MD (1987) Variation in genomic form in plants and its ecological implications. New Phytol 106(Suppl):177-200
11. Bennett MD, Leitch IJ, Price HJ, Johnston JS (2003) Comparison of Caenorhabditis (100 Mb) and Drosophila (175 Mb) using flow cytometry show genome size in Arabidopsis to be (157 Mb) and thus 25% larger than the Arabidopsis Genome Initiative estimate of 125 Mb. Ann Bot 91:547-557
12. Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot 95:127-132
13. Bernardi G (2000a) Isochores and the evolutionary dynamics of vertebrates. Gene 241:3-17
14. Bernardi G (2000b) The compositional evolution of vertebrate genomes. Gene 259:31-43
15. Bernardi G (2007) The neoselectionist theory of genome evolution. Proc Natl Acad Sci U S A 104:8385-8390
16. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953-958
17. Bettecken T, Trifonov EN (2009) Repertoires of the nucleosome-positioning dinucleotides. PLoS One 4:e7654
18. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499-1504
19. Biro JC (2008) Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases. Theor Biol Med Model 5:14
20. Brown TC, Jiricny J (1988) Different base/base mispairs are corrected with different efficiencies and specifities in monkey kidney-cells. Cell 54:705-711
21. Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G (2009) Environmental genomics: a tale of two fishes. Mol Biol Evol 26:1235-1243
22. Bureš P, Wang YF, Horová L, Suda J (2004) Genome size variation in Central European species of Cirsium (Compositae) and their natural hybrids. Ann Bot 94:353-363
23. Bureš P, Šmarda P, Hralová I, Fuentes-Soriano S, Lysák M, Řepka R, Helánová K, Rotreklová O, Procházková J, Úradníček L (2007) Correlation between GC content and genome size in plants. Cytometry 71A:764
24. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154:1819-1825
25. Carels N, Hatey P, Jabbari K, Bernardi G (1998) Compositional properties of homologous coding sequences from plants. J Mol Evol 46:45-53
26. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642-655
27. Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37(Database issue):D93-D97
28. Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A 101:3480-3485
29. Cheng YM, Lin BY (2003) Cloning and characterization of maize B chromosome sequences derived from microdissection. Genetics 164:299-310
30. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ et al (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466:388-392
31. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219
32. Constantini M, Bernardi G (2008a) The short-sequence designs of isochores from the human genome. Proc Natl Acad Sci U S A 105:13971-13976
33. Constantini M, Bernardi G (2008b) Replication timing, chromosomal bands, and isochores. Proc Natl Acad Sci U S A 105:3433-3437
34. Constantini M, Cammarano R, Bernardi G (2009) The evolution of isochore patterns in vertebrate genomes. BMC Genomics 10:146
35. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775-780
36. Crane CF (2007) Patterned sequence in the transcriptome of vascular plants. BMC Genomics 8:173
37. Cruveiller S, Jabbari K, D’Onofrio G, Bernardi G (1999) Different hydrophobicities of orthologous proteins from Xenopus and human. Gene 238:15-21
38. D’Onofrio G, Jabbari K, Bernardi G, Musto H (1999) The correlation of protein hydropathy with the base composition of coding sequences. Gene 238:3-14
39. De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738-754
40. De Rose-Wilson LJ, Gaut BS (2007) Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata. BMC Evol Biol 7:66
41. Doktycz MJ (2002) Nucleic acids: thermal stability and denaturation. In: Encyclopedia of life sciences. Wiley. Wiley Online Library http://onlinelibrary.wiley.com/doi/10.1038/npg.els.0003123
42. Doležel J, Bartoš J (2005) Plant DNA flow cytometry and the estimation of nuclear genome size. Ann Bot 95:99-110
43. Doležel J, Greilhuber J (2010) Nuclear genome size: are we getting closer? Cytometry 77A:635-642
44. Doležel J, Sgorbati S, Lucretti S (1992) Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiol Plantarum 85:625-631
45. Doležel J, Greilhuber J, Suda J (2007) Estimation of nuclear DNA content in plants using flow cytometry. Nat Protoc 2:2233-2244
46. Drouaud J, Camilleri C, Bourguignon PY, Canaguier A, Bérard A, Vezon D, Giancola S, Brunel D, Colot V, Prum B et al (2006) Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”. Genome Res 16:106-114
47. Duret L, Arndt PF (2008) The impact of recombination on nucleotide substitution in the human genome. PLoS Genet 4:e1000071
48. Edwards EJ, Smith SA (2010) Phylogenetic analyses reveal the shady history of C4 grasses. Proc Natl Acad Sci U S A 107: 2532-2537
49. Elhaik E, Landan G, Graur D (2009) Can GC content at third-codon positions be used as a proxy for isochore composition? Mol Biol Evol 26:1829-1833
50. Eyre-Walker A (1993) Recombination and mammalian genome evolution. Proc R Soc Lond B Biol Sci 252:237-243
51. Eyre-Walker A, Hurst LD (2001) The evolution of isochores. Nat Rev Genet 2:549-555
52. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat, a possible mechanism for differentiation of homeologous chromosomes. Genetics 147:1381-1387
53. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X et al (2002) Sequence and analysis of the rice chromosome 4. Nature 420:316-320
54. Ferraro P, Franzolin E, Pontarin G, Reichard P, Bianchi V (2010) Quantification of cellular deoxynucleoside triphosphates. Nucleic Acids Res 38:e85
55. Flagel L, Blackman B (2012) The first ten years of plant genome sequencing and prospects for the next decades. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
56. Frank AC, Lobry JR (1999) Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:65-77
57. Frederico LA, Kunkel TA, Shaw BR (1990) A sensitive genetic assay for the detection of cytosine deamination-determination of rate constants and the activation energy. Biochemistry 29:2532-2537
58. Fullerton SM, Carvalho AB, Clark AG (2001) Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol 18:1139-1142
59. Galtier N, Lobry JR (1997) Relationships between genomic G + C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 44:632-636
60. Godelle B, Cartier D, Marie D, Brown SC, Siljak-Yakovlev S (1993) Heterochromatin study demonstrating the non-linearity of fluorometry useful for calculating genomic base composition. Cytometry 14:618-626
61. Göndör A, Ohlsson R (2009) Chromosome crosstalk in three dimensions. Nature 461:212-217
62. Goodsell DS, Dickerson RE (1994) Bending and curvature calculations in B-DNA. Nucleic Acids Res 22:5497-5503
63. Green P, Ewing B, Mille W, Thomas PJ, NISC Comparative Sequencing Program, Green ED (2003) Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 33:514-517
64. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R (2009) Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 4:e1000079
65. Greilhuber J, Temsch EM, Loureiro JCM (2007) Nuclear DNA content measurement. In: Doležel J, Greilhuber J, Suda J (eds) Flow cytometry with plant cells. Analysis of genes, chromosomes and genomes. Wiley-VCH, Weinheim, pp 67-101
66. Gu W, Zhou T, Wilke C (2010) A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 6:e1000664
67. Guldberg P, Worm J, Grønbæk K (2002) Profiling DNA methylation by melting analysis. Methods 27:121-127
68. Guo X, Bao J, Fan L (2007) Evidence of selectively driven codon usage in rice: implications for GC content evolution of Gramineae genes. FEBS Lett 581:1015-1021
69. Herzel H, Weiss O, Trifonov EN (1999) 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics 15:187-193
70. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W et al (2008) Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 5:183-188
71. Hirsch C, Jiang J (2012) Centromeres: sequence, structure, and biology. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
72. Hosouchi T, Kumekawa N, Tsuruoka H, Kotani H (2002) Physical map-based size of centromeric regions of Arabidopsis thaliana chromosome 1, 2, and 3. DNA Res 9:117-121
73. Hurst LD, Merchant AR (2001) High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis among prokaryotes. Proc R Soc Lond B Biol Sci 268:493-497
74. Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Brief Bioinform 10:609-618
75. Ingle J, Timmis JN, Sinclair J (1975) The relationship between satellite deoxyribonucleic acid, ribosomal ribonucleic acid gene redundancy, and genome size in plants. Plant Physiol 55:496-501
76. International Rice Genome Sequencing Project (2005) The map based sequence of the rice genome. Nature 436:793-800
77. Jabbari K, Bernardi G (2004) Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Gene 333:143-149
78. Jabbari K, Cruveiller S, Clay O, Bernardi G (2003) The correlation between GC3 and hydropathy in human genes. Gene 317:137-140
79. Jaillon CO, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467
80. Janousek B, Hobza R, Vyskot B (2012) Chromosomes and sex differentiation. In: Leitch IJ, Dolezel J, Greilhuber J (eds) Plant genome diversity, vol 2, Physical structure and evolution of plant genomes. Springer, Wien/New York
81. Jansson S, Meyer-Gauen G, Cerff R, MartinW(1994) Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GCcontent change in land-plant nuclear genomes. J Mol Evol 39:34-46
82. Jaramillo-Correa JP, Verdú M, González-Martínez SC (2010) The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol Biol 10:22
83. Jeffares DC, Penkett CJ, Bähler J (2008) Rapidly regulated genes are introns poor. Trends Genet 24:375-378
84. Jeltsch A (2010) Phylogeny of methylomes. Science 328:837-838
85. Jia Q, Wu HT, Zhou XJ, Gao J, Zhao W, Aziz JD, Wei JS, Hou LH, Wu SY, Zhang Y et al (2010) A “GC-rich” method for mammalian gene expression: a dominant role of non-coding DNA GC content in regulation of mammalian gene expression. Sci China Life Sci 53:94-100
86. Kawakami T, Strakosh SC, Zhen Y, Ungerer MC (2010) Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species. Heredity 104:341-350
87. Kejnovsky E, Hawkins J, Feschotte C (2012) Plant transposable elements: biology and evolution. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
88. Kejnovský E, Hobza R, Cermak T, Kubat Z, Vyskot B (2009) The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity 102:533-541
89. King GJ, Ingrouille MJ (1987) Genome heterogenity and classification of the Poaceae. New Phytol 107:633-644
90. Kiyama R, Trifonov EN (2002) What positions nucleosomes?-a model. FEBS Lett 523:7-11
91. Knight RD, Freeland SJ, Landweber LF (2001) A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol 2:research0010.1-0010.13
92. Kovarik A, Dadejova M, Lim YK, Chase MW, Clarkson JJ, Knapp S, Leitch AR (2008) Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigenetics. Ann Bot 101:815-823
93. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ (2009) Amplification free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes. Nat Methods 6:291-295
94. Kubát Z, Hobza R, Vyskot B, Kejnovský E (2008) Microsatellite accumulation on the Y chromosome in Silene latifolia. Genome 51:350-356
95. Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M et al (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16:114-125
96. Lang D, Zimmer AD, Rensing SA, Reski R (2008) Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends Plant Sci 13:542-549
97. Lattorff HMG, Moritz RFA (2008) Recombination rate and AT-content show opposite correlations in mammalian and other animal genomes. J Evol Biol 35:146-149
98. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204-220
99. Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95:9413-9417
100. Leeds JM, Slabaugh MB, Mathews CK (1985) DNA precursor pools and ribonucleotide reductase activity: distribution between the nucleus and cytoplasm of mammalian cells. Mol Cell Biol 5:3443-3450
101. Leitch IJ (2012) Genome size diversity and evolution in land plants. In: Leitch IJ, Dolezel J, Greilhuber J (eds) Plant genome diversity, vol 2, Physical structure and evolution of plant genomes. Springer, Wien/New York
102. Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CMR, D’Hont A, Garsmeur O et al (2008) Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 9:58
103. Li J, Hsia AP, Schnable PS (2007) Recent advances in plant recombination. Curr Opin Plant Biol 10:131-135
104. Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Zhu W, Gu X, Silva JC, Meyers BC, Buell RC (2008) Characterization of paralogous protein families in rice. BMC Plant Biol 8:18
105. Lind P, Andersson DI (2008) Whole genome mutational bias in bacteria. Proc Natl Acad Sci U S A 105:17878-17883
106. Linder PH, Rudall PJ (2005) Evolutionary history of Poales. Annu Rev Ecol Evol Syst 36:107-124
107. Lister R, O’Malley RG, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536
108. Liu QP, Xue QZ (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. J Genet 84:55-62
109. Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS (2009) Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 5:e1000733
110. Liu H, He R, Zhang H, Huang Y, Tian M, Zhang J (2010) Analysis of synonymous codon usage in Zea mays. Mol Biol Rep 37:677-684
111. Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W et al (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 20:1238-1249
112. Lysak M, Schubert I (2012) Mechanisms of chromosome rearrangements. In: Leitch IJ, Dolezel J, Greilhuber J (eds) Plant genome diversity, vol 2, Physical structure and evolution of plant genomes. Springer, Wien/New York
113. Malinska H, Tate JA, Matyasek R, Leitch AR, Soltis DE, Soltis PS (2010) Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids. BMC Evol Biol 10:291
114. Mandáková T, Joly S, Krzywinski M, Mummenhoff K, Lysak MA (2010) Fast diploidization in close mesopolyploid relatives of Arabidopsis. Plant Cell 22:2277-2290
115. Mandel M, Marmur J (1968) Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195-206
116. Mann S, Phoebe-Chen YP (2010) Bacterial genomic G + C composition-eliciting environmental adaptation. Genomics 95:7-15
117. Marie D, Brown SC (1993) A cytometric exercise in plant DNA histograms, with 2C values for 70 species. Biol Cell 78:41-51
118. Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109-118
119. Martomo SA, Mathews CK (2002) Effects of biological DNA precursor pool asymmetry upon accuracy of DNA replication in vitro. Mutat Res-Fund Mol M 499:197-211
120. Matassi G, Montero LM, Salinas J, Bernardi G (1989) The isochore organization and compositional distribution of homologous coding sequences in the nuclear genomes of plants. Nucleic Acids Res 17:5273-5290
121. Meister A, Barow M (2007) DNA base composition of plant genomes. In: Doležel J, Greilhuber J, Suda J (eds) Flow cytometry with plant cells. Analysis of genes, chromosomes and genomes. Wiley-VCH, Weinheim, pp 177-215
122. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245-251
123. Meunier J, Duret L (2004) Recombination drives the evolution of GCcontent in the human genome. Mol Biol Evol 21:984-990
124. Meuth M (1989) The molecular basis of mutations induced by deoxyribonucleoside triphosphate pool imbalances in mammalian cells. Exp Cell Res 181:305-316
125. Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660-1676
126. Michaels ML, Miller JH (1992) The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol 174:6321-6325
127. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-997
128. Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R (2008) Links between core promoter and basic gene features influence gene expression. BMC Genomics 9:92
129. Mrazek J, Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci U S A 95:3720-3725
130. Mukhopadhyay P, Basak S, Ghosh TC (2007) Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes. Gene 400:71-81
131. Musto H, Naya H, Zavala A, Romero H, Alvarez-Valín F, Bernardi G (2004) Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 573:73-77
132. Musto H, Naya H, Zavala A, Romero H, Alvarez-Valín F, Bernardi G (2006) Genomic GC level, optimal growth temperature, and genome size in prokaryotes. Biochem Biophys Res Commun 347:1-3
133. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267
134. Naya H, Romero H, Zavala A, Alvarez B, Musto H (2002) Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes. J Mol Evol 55:260-264
135. Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K et al (2003) Comparative complete genome sequence analysis of the amino acid replacements responsible for thermostability of Corynebacterium efficiens. Genome Res 13:1572-1579
136. Noma K, Nakajima R, Ohtsubo H, Ohtsubo E (1997) RIRE1, a retrotransposon from wild rice Oryza australiensis. Genes Genet Syst 72:131-140
137. Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92-94
138. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L et al (2008) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35:D883-D887
139. Ozkan H, Levy AA, Feldman M (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13:1735-1747
140. Ozkan H, Tuna M, Arumuganathan K (2003) Nonadditive changes in genome size during allopolyploidisation in the wheat (Aegilops-Triticum) group. J Hered 94:260-264
141. Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien MA et al (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186:135-147
142. Pfeifer GP (2006) Mutagenesis at methylated CpG sequences. In: Doerfler W, Böhm P (eds) DNA methylation: basic mechanisms, vol 301, Current topics in microbiology and immunology. Springer, Berlin/Heidelberg/New York, pp 259-281
143. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA et al (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansion in Oryza australensis, a wild relative of rice. Genome Res 16:1262-1269
144. Pozzoli U, Menozzi G, Fumagalli M, Cereda M, Comi GP, Cagliani R, Bresolin N, Sironi M (2008) Both selective and neutral processes drive GC content evolution in the human genome. BMC Evol Biol 8:99
145. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK et al (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329:223-226
146. Pruesse E, Quast C, Knittel K, Fuchs B, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196
147. Puertas MJ (2002) Nature and evolution of B chromosomes in plants: a non-coding but information-rich part of plant genomes. Cytogenet Genome Res 96:198-205
148. Richards C, Verhoeven KJF, Bossdorf O (2012) Evolutionary significance of epigenentic variation. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
149. Robinson JP, Grégori G (2007) Principles of flow cytometry. In: Doležel J, Greilhuber J, Suda J (eds) Flow cytometry with plant cells. Analysis of genes, chromosomes and genomes. Wiley-VCH, Weinheim, pp 19-40
150. Rocha EPC (2004) The replication-related organization of the bacterial chromosome. Microbiology 150:1609-1627
151. Rocha EPC, Danchin A (2002) Competition for scarce resources might bias bacterial genome composition. Trends Genet 18:291-294
152. Rocha EPC, Touchon M, Feil EJ (2006) Similar compositional biases are caused by very different mutational effects. Genome Res 16:1537-1547
153. Romiguier J, Ranwez V, Douzery EJP, Galtier N (2010) Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res 20:1001-1009
154. Salinas J, Matassi G, Montero LM, Bernardi G (1988) Compositional compartmentalization and compositional patterns in the nuclear genomes of plants. Nucleic Acids Res 16:4269-4285
155. Sanford RA, Cole JR, Tiedje JM (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68:893-900
156. SanMiguel P, Vitte C (2009) The LTR-retrotransposons of maize. In: Bennetzen J, Hake S (eds) Handbook of maize genetics and genomics. Springer, New York, pp 307-327
157. SantaLucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95:1460-1465
158. Satapathy SS, Dutta M, Ray SK (2010) Variable correlation of genome GC% with transfer RNA number as well as with transfer RNA diversity among bacterial groups: a-Proteobacteria and Tenericutes exhibit strong positive correlation. Microbiol Res 165:232-242
159. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115
160. Schwartz MN, Trautner TA, Kornberg A (1962) Enzymatic synthesis of deoxyribonucleic acid: XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem 237:1961-1967
161. Seffens W, Digby D (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 27:1578-1584
162. Segal E, Fondufe-Mittendorf Y, Chen L, Thåström AC, Field Y, Moore IK, Wang JPZ, Widom J (2006) A genomic code for nucleosome positioning. Nature 442:772-778
163. Serenkov GP (1962) Nucleic acids in the evolution of algae [in Russiian]. Izv Akad Nauk SSSR Biol 1962:857-868
164. Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749-1759
165. Shantz HL (1954) The place of grasslands in the Earths cover of vegetation. Ecology 35:143-145
166. Shapiro HS (1976) Distribution of purines and pyrimidines in deoxyribonucleic acids. In: Fasman GD (ed) Handbook of biochemistry and molecular biology, 3rd edn. CRCPress, Cleveland, pp 241-281
167. Shi XL, Wang XY, Li Z, Zhu Q, Yang J, Ge S, Luo J (2007) Evidence that natural selection is the primary cause of the guanine-cytosine content variation in rice genes. J Integr Plant Biol 49:1393-1399
168. Siomos M, Riha K (2012) Telomeres and their biology. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
169. Sloan DB, Taylor DR (2010) Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing. J Mol Evol 70:479-491
170. Šmarda P, Bureš P, Horová L (2010) The evolution of base composition in monocots. In: Proceedings of the international workshop on structural and functional diversity of the eukaryotic genome, Brno. Muni Press, Brno, p 69
171. Šmarda P, Bureš P, Horová L, Foggi B, Rossi G (2008) Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction. Ann Bot 101:421-433
172. Šmarda P, Bureš P, Šmerda J, Horová L (2012) Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability. New Phytol 193:513-521
173. Smith DR (2009) Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol Biol 71:627-639
174. Stalder L, Mühlemann O (2008) The meaning of nonsense. Trends Cell Biol 18:315-321
175. Sterpone F, Bertonati C, Briganti G, Melchionna S (2010) Water around thermophilic proteins: the role of charged and apolar atoms. J Phys Condens Matter 22:284113
176. Svejstrup JQ (2002) Mechanisms of transcription-coupled DNA repair. Nat Rev Mol Cell Biol 3:21-29
177. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L et al (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009-D1014
178. Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA (2010) GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 11:308
179. Tillo D, Hughes TR (2009) G plus C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10:442
180. Touchon M, Arneodo A, d’Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32:4969-4978
181. Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci U S A 77:3816-3820
182. Trivedi S, Rao SR, Gehlot HS (2005) Nucleic acid stability in thermophilic prokaryotes: a review. J Cell Mol Biol 4:61-69
183. Troukhan M, Tatarinova T, Bouck J, Flawell R, Alexandrov N (2009) Genome-wide discovery of cis-elements in promoter sequences using gene expression data. OMICS 13:139-151
184. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169-179
185. Vanyushin B (2006) DNA methylation in plants. In: Doerfler W, Böhm P (eds) DNA methylation: basic mechanisms, vol 2. Springer, Berlin/Heidelberg/New York, pp 67-122
186. Varriale A, Torelli G, Bernardi G (2008) Compositional properties and thermal adaptation of 18S rRNA in vertebrates. RNA 14:1492-1500
187. Veselý P, Bureš P,Šmarda P, Pavlíček T (2012) Genome size and DNA base composition of geophytes: the mirror of phenology and ecology? Ann Bot 109:65-75
188. Vetsigian K, Goldenfeld N (2009) Genome rhetoric and the emergence of compositional bias. Proc Natl Acad Sci U S A 106:215-220
189. Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65:1-43
190. Vinogradov AE (1998) Genome size and GC-percent in vertebrates as determined by flow cytometry: the triangular relationship. Cytometry 31:100-109
191. Vinogradov AE (2001) Within-intron correlation with base composition of adjacent exons in different genomes. Gene 276:143-151
192. Vinogradov AE (2003) DNA helix: the importance of being GC-rich. Nucleic Acids Res 31:1838-1844
193. Vinogradov AE (2004) Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet 20:248-253
194. Vinogradov AE (2005) Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res 33:559-563
195. Watson JM, Riha K (2010) Comparative biology of telomeres: where plants stand. FEBS Lett 584:3752-3759
196. Wolf P (2012) Plastid genome diversity. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
197. Wolfe KH, Sharp PM, Li W-H (1989) Mutation rates differ among regions of the mammalian genome. Nature 337:283-285
198. Wong GKS, Wang J, Tao L, Tan J, Zhang JG, Passey DA, Yu J (2002) Compositional gradients in Gramineae genes. Genome Res 12:851-856
199. Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Basestacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34:564-574
200. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J 63:353-365
201. Yang C, Bolotin E, Jiang T, Sladek FM, Martinez M (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389:52-65
202. Yu J, Hu S, Wang J, Wong GKS, 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
203. Zhang X (2008) The epigenetic landscape of plants. Science 320:489-492
204. Zhang X (2012) Chromatin modifications. In: Wendel JF (ed) Plant genome diversity, vol 1, Plant genomes, their residents, and their evolutionary dynamics. Springer, Wien/New York
205. Zhang R, Zhang CT (2004) Isochore structures in the genome of the plant Arabidopsis thaliana. J Mol Evol 59:227-238
206. Zhang L, Kosakovsky Pond S, Gaut BS (2001) A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J Mol Evol 52:144-156
207. Zhang C, Li WH, Krainer AR, Zhang MQ (2008) RNA landscape of evolution of optimal exon and intron discrimination. Proc Natl Acad Sci U S A 105:5797-5802