title: Use of methylation filtration and C(0)t fractionation for analysis of genome composition and comparative genomics in bread wheat.
abstract: 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.
authors.affiliation: Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, India.
authors.forename: Rajib
authors.initials: R
authors.lastname: Bandopadhyay
authors.forename: Sachin
authors.initials: S
authors.lastname: Rustgi
authors.forename: Rajat Kanti
authors.initials: RK
authors.lastname: Chaudhuri
authors.forename: Paramjit
authors.initials: P
authors.lastname: Khurana
authors.forename: Jitendra Paul
authors.initials: JP
authors.lastname: Khurana
authors.forename: Akhilesh Kumar
authors.initials: AK
authors.lastname: Tyagi
authors.forename: Harindra Singh
authors.initials: HS
authors.lastname: Balyan
authors.forename: Andreas
authors.initials: A
authors.lastname: Houben
authors.forename: Pushpendra Kumar
authors.initials: PK
authors.lastname: Gupta
mesh_terms: D001939:Bread; D055028:Comparative Genomic Hybridization; D004247:DNA / Q000235:genetics; D019175:DNA Methylation; D004251:DNA Transposable Elements; D020224:Expressed Sequence Tags; D005374:Filtration; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D018598:Minisatellite Repeats; D016366:Open Reading Frames; D012275:Oryza / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D014908:Triticum / Q000235:genetics*; D003313:Zea mays / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D022661:RNA, Untranslated; D004247:DNA