Dataset Information

Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis.

ABSTRACT: BACKGROUND: 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, approximately 30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, approximately 60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, approximately 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.

SUBMITTER: Srivastava J

PROVIDER: S-EPMC2346481 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis.

Srivastava Jyoti J Premi Sanjay S Kumar Sudhir S Ali Sher S

BMC genomics 20080320

<h4>Background</h4>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 ...[more]

PMID: 18366692

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Project description:BACKGROUND: Transcriptionally quiescent spermatozoa have been established to be a repository of mRNA coding for several functionally essential cellular proteins. This entourage of mRNA is envisaged to be involved in post-fertilization and early embryogenesis. Minisatellites tagged with mRNA transcripts have been implicated with gene organization, regulation and function. However, the organization and expression of the minisatellite tagged transcript diversity, particularly in spermatozoa, remains unclear. RESULTS: In the present study, we identified and characterized 12 mRNA transcripts from the spermatozoa of water buffalo Bubalus bubalis employing minisatellite associated sequence amplification (MASA) and a consensus sequence of 33.15 repeat loci. Of these 33.15 tagged transcripts, only one was found to be homologous to Bovine steroid 21-hydroxylase (P-450-c21) gene. Other ten transcripts showed significant similarity with various mRNAs or chromosomal contigs across the species. The remaining one construed to be novel since this was unreported in the database (NCBI GenBank). All these uncharacterized and known transcripts showed highest expression in testis and spermatozoa compared to that in somatic tissues and ovary. Of these 12 mRNA transcripts, 4 showed differential expression in the forebrain and hindbrain of buffalo. Moreover, genes corresponding to all the 33.15 tagged spermatozoal transcripts were found to be conserved across 13 other species analyzed. CONCLUSION: Our results show MASA as an important tool to capture mRNA transcript diversity tagged with minisatellites in the spermatozoa. Comprehensive characterization of these transcripts is envisaged to augment our understanding on the genes involved in testicular functions and sustenance of a viable paternal genome during pre- and post- fertilization events and early stages of development. Prospects of this approach in genome analysis in general and comparative genomics in particular are highlighted.

Project description:Toxoplasmosis and neosporosis are diseases with worldwide distribution that are associated with reproductive problems in livestock and responsible for economic losses. This review presents an overview of the current knowledge relative to these diseases in water buffalo (Bubalus bubalis). In general, buffalo are considered resistant to clinical toxoplasmosis because there are studies only reporting serological evidence of natural infection in these animals. Studies have described age, poor hygienic status of the farm, and presence of cats as risk factors for the development of Toxoplasma gondii infection in buffalo. It must be highlighted that buffalo meat, which does not receive adequate freezing treatment, could be a potential source for toxoplasmic human infection as well as the importance of raw buffalo milk in the transmission of toxoplasmosis to human beings. Neospora caninum is considered one of the major causes of abortion and responsible for huge economic losses in cattle. Vertical transmission is the main route to infect calves, and is responsible for maintaining the parasite within a herd. In buffalo, vertical transmission is also described; moreover, although there are indications that N. caninum may be associated with abortion in dairy buffalo, the reproductive importance of neosporosis is apparently lower in buffalo relative to cattle. Most studies have identified a higher time of exposition to N. caninum oocysts relative to age. The household system was also described as a risk factor for infection, possibly due to persistent contact between the home-raised buffalo and canids. The fetal immune competence of buffalo is similar to bovine, and buffalo fetus are highly susceptible to infection during the first trimester of pregnancy, indicating that N. caninum may be an abortigenic agent in buffaloes. Alternatively, it is interesting to note there is evidence that the inflammatory response in pregnant buffalo infected with N. caninum is mild enough to avoid abortion in most cases. It is proposed that the possible transmission of toxoplasmosis through unprocessed milk and buffalo meat may occur, which is important in terms of public health. Additionally, there is strong evidence to suggest that N. caninum may be associated with abortion in buffalo.

Dataset Information

Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis.

Publications

Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis.

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