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dc.creatorSrivastava, J
dc.creatorPremi, S
dc.creatorKumar, S
dc.creatorAli, S
dc.date.accessioned2021-02-01T22:01:59Z
dc.date.available2021-02-01T22:01:59Z
dc.date.issued2008-03-20
dc.identifier.issn1471-2164
dc.identifier.issn1471-2164
dc.identifier.doihttp://dx.doi.org/10.34944/dspace/5591
dc.identifier.other18366692 (pubmed)
dc.identifier.urihttp://hdl.handle.net/20.500.12613/5609
dc.description.abstractBackground: Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in the best characterized organisms including human, remains unclear. The main objective of this study was to explore the buffalo transcriptome for its association with GACA/GATA repeats, and study the structural organization and differential expression of the GACA/GATA repeat tagged transcripts. Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution. Results: We explored several genomes and transcriptomes, and observed total absence of these repeats in the prokaryotes, with their gradual accumulation in higher eukaryotes. Further, employing novel microsatellite associated sequence amplification (MASA) approach using varying length oligos based on GACA and GATA repeats; we identified and characterized 44 types of known and novel mRNA transcripts tagged with these repeats from different somatic tissues, gonads and spermatozoa of water buffalo Bubalus bubalis. GACA was found to be associated with higher number of transcripts compared to that with GATA. Exclusive presence of several GACA-tagged transcripts in a tissue or spermatozoa, and absence of the GATA-tagged ones in lung/heart highlights their tissue-specific significance. Of all the GACA/GATA tagged transcripts, ∼30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, ∼60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, ∼75% GACA-tagged and all the GATA-tagged transcripts were found to be conserved across the species. Conclusion: Present study is a pioneer attempt exploring GACA/GATA tagged transcriptome in any mammalian species highlighting their tissue, stage and species-specific expression profiles. Comparative analysis suggests the gradual accumulation of these repeats in the higher eukaryotes, and establishes the GACA richness of the buffalo transcriptome. This is envisaged to establish the roles of integral simple sequence repeats and tagged transcripts in gene expression or regulation. © 2008 Srivastava et al; licensee BioMed Central Ltd.
dc.format.extent132-132
dc.language.isoen
dc.relation.haspartBMC Genomics
dc.relation.isreferencedbySpringer Science and Business Media LLC
dc.rightsCC BY
dc.subjectAmino Acid Sequence
dc.subjectAnimals
dc.subjectBase Sequence
dc.subjectBlotting, Northern
dc.subjectBlotting, Southern
dc.subjectBuffaloes
dc.subjectDNA Primers
dc.subjectEvolution, Molecular
dc.subjectGene Dosage
dc.subjectGene Expression Profiling
dc.subjectGenomics
dc.subjectIn Situ Hybridization, Fluorescence
dc.subjectMale
dc.subjectMinisatellite Repeats
dc.subjectMolecular Sequence Data
dc.subjectPolymorphism, Single Nucleotide
dc.subjectReverse Transcriptase Polymerase Chain Reaction
dc.subjectSequence Alignment
dc.subjectSequence Analysis, DNA
dc.subjectSpecies Specificity
dc.subjectSpermatozoa
dc.titleOrganization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis
dc.typeArticle
dc.type.genreJournal Article
dc.relation.doi10.1186/1471-2164-9-132
dc.ada.noteFor Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.edu
dc.creator.orcidKumar, Sudhir|0000-0002-9918-8212
dc.date.updated2021-02-01T22:01:56Z
refterms.dateFOA2021-02-01T22:01:59Z


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