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

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)

These authors contributed equally to this work.

摘要

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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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doi: 10.1016/j.jgg.2011.06.003

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

Corresponding author: E-mail address: pkgupta36@gmail.com (Pushpendra Kumar Gupta)

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doi: 10.1016/j.jgg.2011.06.003

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

Corresponding author: E-mail address: pkgupta36@gmail.com (Pushpendra Kumar Gupta)

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