Use of methylation filtration and C(0)t fractionation for analysis of genome composition and comparative genomics in bread wheat

We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C(0)t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC...

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Published in:Journal of genetics and genomics 2011-07, Vol.38 (7), p.315-325
Main Authors: Bandopadhyay, Rajib, Rustgi, Sachin, Chaudhuri, Rajat Kanti, Khurana, Paramjit, Khurana, Jitendra Paul, Tyagi, Akhilesh Kumar, Balyan, Harindra Singh, Houben, Andreas, Gupta, Pushpendra Kumar
Format: Article
Language:English
Subjects:
Bread
Comparative Genomic Hybridization
DNA - genetics
DNA Methylation
DNA Transposable Elements
Expressed Sequence Tags
Filtration
Genome, Plant - genetics
Genomics
In Situ Hybridization, Fluorescence
Minisatellite Repeats
Open Reading Frames
Oryza - genetics
RNA, Untranslated - genetics
Triticum - genetics
Zea mays - genetics
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Summary:We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C(0)t 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 C(0)t (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.
ISSN:1673-8527
DOI:10.1016/j.jgg.2011.06.003