Use of methylation filtration and C0t fractionation for analysis of genome composition and comparative genomics in bread wheat

Rajib Bandopadhyay; Sachin Rustgi; Rajat Kanti Chaudhuri; Paramjit Khurana; Jitendra Paul Khurana; Akhilesh Kumar Tyagi; Harindra Singh Balyan; Andreas Houben; Pushpendra Kumar Gupta

doi:10.1016/j.jgg.2011.06.003

Volume 38 Issue 7

Jul. 2011

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Article Navigation > Journal of Genetics and Genomics > 2011 > 38(7): 315-325

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Use of methylation filtration and C0t fractionation for analysis of genome composition and comparative genomics in bread wheat

doi: 10.1016/j.jgg.2011.06.003

a
Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut 250004, India
b
Department of Biotechnology, Birla Institute of Technology, Mesra 835215, Ranchi, India
c
Department of Crop & Soil Sciences, Washington State University, Pullman 99163, USA
d
Department of Botany, University of Calcutta, Kolkata 700019, India
e
Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
f
Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse-03, Gatersleben 06466, Germany

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Corresponding author: E-mail address: pkgupta36@gmail.com (Pushpendra Kumar Gupta)
Received Date: 2010-11-16
Accepted Date: 2011-06-13
Rev Recd Date: 2011-06-08

Available Online: 2011-06-20

Publish Date: 2011-07-20

Abstract

Abstract

We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C₀t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences (e.g., transposable elements and simple sequence repeats), protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/exclusion in methylation-filtered (MF) library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags (ESTs) available in the public domain. Only a limited overlap among MF, high C₀t (HC), and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.
- Methylation–filtration,
- Transposable elements,
- Gene-rich regions

These authors contributed equally to this work.

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References(59)

References

[1]	Bedell, J.A., Budiman, M.A., Nunberg, A. et al. Sorghum genome sequencing by methylation filtration PLoS Biol., 3 (2005),p. e13
[2]	Birren, B., Green, D., Myers, M.R. et al.
[3]	Bryan, C.J., Collins, A.J., Stephenson, P. et al. Isolation and characterization of microsatellites from hexaploid bread wheat Theor. Appl. Genet., 94 (1997),pp. 557-563
[4]	Carels, N., Bernardi, G. Two classes of genes in plants Genetics, 154 (2000),pp. 1819-1825
[5]	Chan, A.P., Melake-Berhan, A., O’Brien, K. et al. BMC Genomics, 12 (2008),p. 282
[6]	Cuadrado, A., Schwarzacher, T. The chromosomal organization of simple sequence repeats in wheat and rye genomes Chromosoma, 107 (1998),pp. 587-594
[7]	Cuadrado, A., Cardoso, M., Jouve, N. Physical organization of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications Cytogenet. Genome Res., 120 (2008),pp. 210-219
[8]	Devos, K.M., Ma, J., Pontaroli, A.C. et al. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat Proc. Natl. Acad. Sci. USA, 102 (2005),pp. 19243-19248
[9]	Echenique, V., Stamova, B., Wolters, P. et al. Theor. Appl. Genet., 104 (2002),pp. 840-844
[10]	Erayman, M., Sandhu, D., Sidhu, D. et al. Demarcating gene-rich regions of the wheat genome Nucleic Acids Res., 32 (2004),pp. 3546-3565
[11]	Fellers, J.P. Genome filtering using methylation-sensitive restriction enzymes with six base pair recognition sites Plant Genome, 1 (2008),pp. 146-152
[12]	Fu, Y., Hsia, A.P., Guo, L. et al. Plant Physiol., 135 (2004),pp. 2040-2045
[13]	Gill, B.S., Friebe, B.
[14]	Gonzalez, I.L., Sylvester, J.E. Incognito rRNA and rDNA in databases and libraries Genome Res., 7 (1997),pp. 65-70
[15]	Gustafson, A.M., Allen, E., Givan, S. et al. Nucl. Acids Res., 33 (2005),pp. D637-D640
[16]	Houben, A., Field, B.L., Saunders, V. Microdissection and chromosome painting of plant B chromosomes Methods Cell Sci., 23 (2001),pp. 115-124
[17]	Jakše, J., Meyer, J.D., Suzuki, G. et al. Pilot sequencing of onion genomic DNA reveals fragments of transposable elements, low gene densities, and significant gene enrichment after methyl filtration Mol. Genet. Genomics, 280 (2008),pp. 287-292
[18]	Kashkush, K., Feldman, M., Levy, A.A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat Nat. Genet., 33 (2003),pp. 102-106
[19]	Kumar, S., Singh, C.K., Bandopadhyay, R. Wheat genome sequence: challenges and success Curr. Sci., 100 (2011),pp. 455-457
[20]	La Rota, M., Kantety, R.V., Yu, J.K. et al. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley BMC Genomics, 6 (2005),p. 23
[21]	Lakey, N., Budiman, M.A., Nunberg, A., Citek, R., and Bedell, J.,2004. Methylation “filtering” to enrich for coding sequence regions. In: International Cotton Genome Initiative ICGI–2004 Workshop, October 10–13, Hyderabad, Andhra Pradesh, India, 166.
[22]	Lamoureux, D., Peterson, D.G., Li, W. et al. Genome, 48 (2005),pp. 1120-1126
[23]	Langdon, T., Thomas, A., Huang, L. et al. BMC Plant Biol., 9 (2009),p. 70
[24]	Li, W., Zhang, P., Fellers, J.P. et al. Sequence composition, organization, and evolution of the core Triticeae genome Plant J., 40 (2004),pp. 500-511
[25]	Messeguer, R., Ganal, M.W., Steffens, J.C. et al. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA Plant Mol. Biol., 16 (1991),pp. 753-770
[26]	Messing, J., Bharti, A.K., Karlowski, W.M. et al. Sequence composition and genome organization of maize Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 14349-14354
[27]	Mette, M.F., Van Der Winden, J., Matzke, M. et al. Plant Physiol., 130 (2002),pp. 6-9
[28]	Meyers, B.C., Tingey, S.V., Morgante, M. Abundance, distribution and transcriptional activity of repetitive elements in the maize genome Genome Res., 11 (2001),pp. 1660-1676
[29]	Morgante, M., Hanafey, M., Powell, W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat. Genet., 30 (2002),pp. 194-200
[30]	Palmer, L.E., Rabinowicz, P.D., O’shaughnessy, A.L. et al. Maize genome sequencing by methylation filtration Science, 302 (2003),pp. 2115-2117
[31]	Paterson, A., Wicker, T., Rong, J., Estill, J., and Peterson, D.G, 2004. Efficient sequencing and assembly of the cotton genome, Incorporating Cot – based cloning and sequencing. In: International Cotton Genome Initiative ICGI–2004 Workshop, October 10–13, Hyderabad, Andhra Pradesh, India, 167.
[32]	Paux, E., Sourdille, P., Salse, J. et al. A physical map of the 1-gigabase bread wheat chromosome 3B Science, 322 (2008),pp. 101-104
[33]	Peterson, D.G., Schulze, S.R., Sciara, E.B. et al. Genome Res., 12 (2002),pp. 795-807
[34]	Qi, L.L., Echalier, B., Chao, S. et al. A chromosome bin map of 16,000 EST loci and distribution of genes among the three genomes of polyploid wheat Genetics, 168 (2004),pp. 701-712
[35]	Röder, M.S., Korzun, V., Gill, B.S. et al. The physical mapping of microsatellites markers in wheat Genome, 41 (1998),pp. 278-283
[36]	Rabinowicz, P.D., Citek, R., Budiman, M.A. et al. Differential methylation of genes and repeats in land plants Genome Res., 15 (2005),pp. 1431-1440
[37]	Rushton, P.J., Bokowiec, M.T., Han, S. et al. Tobacco transcription factors: novel insights into transcriptional regulation in the Solanaceae Plant Physiol., 147 (2008),pp. 280-295
[38]	Sabot, F., Guyot, R., Wicker, T. et al. Updating of transposable element annotations from large wheat genomic sequences reveals diverse activities and gene associations Mol. Genet. Genomics, 274 (2005),pp. 119-130
[39]	Safár, J., Bartos, J., Janda, J. et al. Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat Plant J., 39 (2004),pp. 960-968
[40]	Safár, J., Simková, H., Kubaláková, M. et al. Development of chromosome-specific BAC resources for genomics of bread wheat Cytogenet. Genome Res., 129 (2010),pp. 211-223
[41]	Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A. et al. Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics Proc. Natl. Acad. Sci. USA, 81 (1984),pp. 8014-8018
[42]	Salse, J., Bolot, S., Throude, M. et al. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution Plant Cell, 20 (2008),pp. 11-24
[43]	Sambrook, J., Russell, D.W.
[44]	Schmidt, T., Heslop-Harrison, J.S. The physical and genomic organization of microsatellites in sugar beet Proc. Natl. Acad. Sci. USA, 93 (1996),pp. 8761-8765
[45]	Singh, N.K., Dalal, V., Batra, K. et al. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes Funct. Integr. Genomics, 7 (2007),pp. 17-35
[46]	Springer, N.M., Xu, X., Barbazuk, W.B. Utility of different gene-enrichment approaches towards identifying and sequencing the maize gene space Plant Physiol., 136 (2004),pp. 3023-3033
[47]	Timko, M.P., Rushton, P.J., Laudeman, T.W. et al. Sequencing and analysis of the gene-rich space of cowpea BMC Genomics, 9 (2008),p. 103
[48]	Topp, C.N., Zhong, C.X., Dawe, R.K. Centromere-encoded RNAs are integral components of the maize kinetochore Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 15986-15991
[49]	Van der Hoeven, R., Ronning, C., Giovannoni, J. et al. Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing Plant Cell, 14 (2002),pp. 1441-1456
[50]	Vicient, C.M., Jaaskelainen, M., Kalendar, R. et al. Active retrotransposons are a common feature of grass genomes Plant Physiol., 125 (2001),pp. 1282-1292
[51]	Wang, Z., Gerstein, M., Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics Nat. Rev. Genet., 10 (2009),pp. 57-63
[52]	Whitelaw, C.A., Barbazuk, W.B., Pertea, G. et al. Enrichment of gene-coding sequences in maize by genome filtration Science, 302 (2003),pp. 2118-2120
[53]	Wong, G.K.S., Wang, J., Tao, L. et al. Compositional gradients in Gramineae genes Genome Res., 12 (2002),pp. 851-856
[54]	Yu, J., Hu, S., Wang, J. et al. Science, 296 (2002),pp. 79-91
[55]	Yuan, Y., Sanmiguel, P.J., Bennetzen, J.L. Plant J., 34 (2003),pp. 249-255
[56]	Zhang, L.Y., Bernard, M., Leroy, P. et al. High transferability of bread wheat EST-derived SSRs to other cereals Theor. Appl. Genet., 111 (2005),pp. 677-687
[57]	Zhang, X., Yazaki, J., Sundaresan, A. et al. Cell, 126 (2006),pp. 1189-1201
[58]	Zilberman, D., Gehring, M., Tran, R.K. et al. Nat. Genet., 39 (2007),pp. 61-69
[59]	Šimková, H., Janda, J., Hřibová, E. et al. Cot-based cloning and sequencing of the short arm of wheat chromosome 1B Plant Soil Environ., 53 (2007),pp. 437-441