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

First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)

Dinoflagellates are a group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in the nucleus of Gambierdiscus australes. The results showed an increased relative abundance of the different microsatellite motifs with increasing GC content. Two ND-FISH probes, (A)₂₀ and (AAT)₅ , did not yield signals whereas the remainder revealed a dispersed but nonrandom distribution of the microsatellites, mostly in clusters. The bean-shaped interphase nucleus of G. australes contained a region with a high density of trinucleotides. This nuclear compartment was located between the nucleolar organizer region (NOR), located on the concave side of the nucleus, and the convex side. Telomeric DNA was grouped in multiple foci and distributed in two polarized compartments: one associated with the NOR and the other peripherally located along the convex side of the nucleus. Changes in the position of the telomeres during cell division evidenced their dynamic distribution and thus that of the chromosomes during dinomitosis. These insights into the spatial organization of microsatellites and telomeres and thus into the nuclear architecture of G. australes will open up new lines of research into the structure and function of the nucleosome-less chromatin of dinoflagellates.

Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes

The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.

Advances in reproductive biotechnologies

In recent times, reproductive biotechnologies have emerged and started to replace the conventional techniques. It is noteworthy that for sustained livestock productivity, it is imperative to start using these techniques for facing the increasing challenges for productivity, reproduction and health with impending environment conditions. These recent biotechniques, both in male and female, have revolutionized and opened avenues for studying and manipulating the reproductive process both in vitro and in vivo in various livestock species for improving tis efficiency. This review attempts to highlight pros and cons, on the recent developments in reproductive biotechnologies, both in male and female in livestock species.

Karyotypic variation of Glanidium ribeiroi Haseman, 1911 (Siluriformes, Auchenipteridae) along the Iguazu river basin

Abstract The Iguazu river is a tributary of the left margin of the Paraná river, isolated from this basin about 22 million years ago with the appearance of the Iguazu Falls. The Iguazu river is characterized by high endemism due to two factors: its rugged topography and the old isolation caused by formation of the Iguazu Falls. This study analyzed cytogenetically a population of Glanidium ribeiroi collected in a region at the final stretch of this basin, by Giemsa staining, C-banding, impregnation by silver nitrate, and FISH with probes of 5S rDNA, 18S rDNA, telomeric sequence [TTAGGG]n, and [GATA]n repeats. The diploid number was equal to 58 chromosomes. The heterochromatin was present in the terminal region of almost all chromosomes. The Ag-NORs were simple and presented interstitially on the short arm of the submetacentric pair 14, which was confirmed by FISH with 18S rDNA probe. The 5S rDNA-FISH marked only the submetacentric pair 16 on the long arm in interstitial position. The FISH with [TTAGGG]n probe presented all telomeres labeled as expected, with an absence of Interstitial Telomeric Sequence (ITS). The repetitive [GATA]n sequence was dispersed throughout the genome, with preferential location in the terminal region of all chromosomes. The data obtained are discussed herein with other species of Auchenipteridae, and other previously analyzed populations of G. ribeiroi from the Iguazu river, verifying differences among these populations, which should be mainly related to the rugged topography of this basin.

Transcriptional dynamics of homeobox C11 gene in water buffalo bubalus bubalis

The Hox complex contains 39 genes clustered into four groups involved in cell differentiation and development. We cloned full-length sequence of Hoxc11 gene from water buffalo Bubalus bubalis, assessed its copy number, localized the same onto the chromosome 5, and studied its evolutionary conservation across the species. Northern hybridization of Hoxc11 showed a 2.2 kb band in the tissues analyzed. Real-Time PCR showed highest expression of Hoxc11 gene in lung followed by spleen, spermatozoa, and testis. Six interacting partners of this gene showed higher expression in spleen, lung, testis, and spermatozoa. During the early stages of development, Hoxc11 and its interacting partners both showed lower expression, which then became prominent during the age of 1-3 years, regressed drastically thereafter, and remained so until the animal's life time (∼ 20 years). The high expression of Hoxc11 and its interacting partners in spermatozoa and testis during the onset of puberty suggests its likely role in the differentiation of gonads and subsequent reproductive activities. Additional work on Hoxc11 especially, in the context of respiratory, immunological, and in/fertility in other species, including humans would be useful for establishing its broader biological significance towards the enrichment of functional and comparative genomics.

The role of chromosomal fusion in the karyotypic evolution of the genus Ageneiosus (Siluriformes: Auchenipteridae)

Ageneiosus is the most widely distributed genus of the family Auchenipteridae among South American river basins. Although chromosome studies in the family are scarce, this genus has the largest number of analyzed species, with 2n = 54 to 56 chromosomes, differing from the rest of the family (2n = 58). This study aimed to analyze Ageneiosus inermis from the Araguaia River basin. The diploid number found was of 56 chromosomes. Heterochromatin was allocated in terminal region of most chromosomes, plus a pericentromeric heterochromatic block in pair 1, a pair distinguished by size in relation to other chromosomes pairs. AgNORs were detected in only one submetacentric chromosome pair, which was confirmed by FISH. 5S rDNA was present in only one metacentric chromosome pair. Hybridization with [TTAGGG]n sequence marked the telomeres of all chromosomes, in addition to an ITS in the proximal region of the short arm of pair 1. The repetitive [GATA]n sequence was dispersed, with preferential location in terminal region of the chromosomes. Ageneiosus has a genomic organization somewhat different when compared to other Auchenipteridae species. Evidences indicate that a chromosomal fusion originated the first metacentric chromosome pair in A. inermis, rearrangement which may be a basal event for the genus

Molecular mining of GGAA tagged transcripts and their expression in water buffalo Bubalus bubalis

Repeat sequences are involved in regulation of gene expression both at the transcriptional and translational level. In the mammalian genomes, tri- and tetranucleotide repeats like ATA, AATA, GGAA and GAAA have been associated with diseases. In silico analysis of (GGAA)5 distribution across the species showed maximum number of this repeat in the mouse transcriptome compared to that in other species. Following this, we conducted minisatellite associated sequence amplification (MASA) to explore the buffalo's transcriptome using cDNA from different tissues and an oligo based on (GGAA)5 repeats. MASA uncovered twenty six mRNA transcripts showing homology to known genes in the database. qPCR studies showed the highest expression of twelve transcripts in the spleen. A transcript, pLRC107 with its partial sequence of 203 nucleotides showed sequence variation at several positions in spleen as compared to other four tissues examined. Transcript pLRC100 was found to represent the partial coding sequence of Bos taurus HECT {(homologous to E6-associated protein (UBE3A) carboxyl-terminus domain) and RCC1 (CHC1)-like domain (RLD) 1}, mRNA. We ascertained full length coding sequence of HECT gene and localized the same on buffalo chromosome 10 employing FISH. This gene was found to be conserved across the species. Another gene LRP8 uncovered in the process showed copy number variation between buffalo males (4-9) and females (34-54). The MASA approach enabled us to identify several genes in Bubalus bubalis without screening an entire cDNA library. The highest expression of 12 mRNA transcripts in spleen suggests their likely involvement with immuno transaction. A comprehensive knowledge of the repeat tagged transcriptomes is envisaged to help in understanding their significance in genome organization and evolution forming rich basis of functional and comparative genomics.

Molecular mining of alleles in water buffalo Bubalus bubalis and characterization of the TSPY1 and COL6A1 genes

Background

Minisatellites are an integral part of eukaryotic genomes and show variation in the complexity of their organization. Besides their presence in non-coding regions, a small fraction of them are part of the transcriptome, possibly participating in gene regulation, expression and silencing. We studied the minisatellite (TGG)_n tagged transcriptome in the water buffalo Bubalus bubalis across various tissues and the spermatozoa, and characterized the genes TSPY1 and COL6A1 discovered in the process.

Results

Minisatellite associated sequence amplification (MASA) conducted using cDNA and oligonucleotide primer (TGG)₅ uncovered 38 different mRNA transcripts from somatic tissues and gonads and 15 from spermatozoa. These mRNA transcripts corresponded to several known and novel genes. The majority of the transcripts showed the highest level of expression either in the testes or spermatozoa with exception of a few showing higher expression levels in the lungs and liver. Transcript SR1, which is expressed in all the somatic tissues and gonads, was found to be similar to the Bos taurus collagen type VI alpha 1 gene (COL6A1). Similarly, SR29, a testis-specific transcript, was found to be similar to the Bos taurus testis-specific Y-encoded protein-1 representing cancer/testis antigen 78 (CT78). Subsequently, full length coding sequences (cds) of these two transcripts were obtained. Quantitative PCR (q-PCR) revealed 182-202 copies of theTSPY1 gene in water buffalo, which localized to the Y chromosome.

Conclusions

The MASA approach enabled us to identify several genes, including two of clinical significance, without screening an entire cDNA library. Genes identified with TGG repeats are not part of a specific family of proteins and instead are distributed randomly throughout the genome. Genes showing elevated expression in the testes and spermatozoa may prove to be potential candidates for in-depth characterization. Furthermore, their possible involvement in fertility or lack thereof would augment animal biotechnology.

RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

BACKGROUND

Repetitive sequences are the major components of the eukaryotic genomes. Association of these repeats with transcribing sequences and their regulation in buffalo Bubalus bubalis has remained largely unresolved.

RESULTS

We cloned and sequenced RsaI repeat fragments pDp1, pDp2, pDp3, pDp4 of 1331, 651, 603 and 339 base pairs, respectively from the buffalo, Bubalus bubalis. Upon characterization, these fragments were found to represent retrotransposons and part of some functional genes. The resultant clones showed cross hybridization only with buffalo, cattle, goat and sheep genomic DNA. Real Time PCR, detected ~2 × 10(4) copies of pDp1, ~ 3000 copies of pDp2 and pDp3 and ~ 1000 of pDp4 in buffalo, cattle, goat and sheep genomes, respectively. RsaI repeats are transcriptionally active in somatic tissues and spermatozoa. Accordingly, pDp1 showed maximum expression in lung, pDp2 and pDp3 both in Kidney, and pDp4 in ovary. Fluorescence in situ hybridization showed repeats to be distributed all across the chromosomes.

CONCLUSIONS

The data suggest that RsaI repeats have been incorporated into the exonic regions of various transcribing genes, possibly contributing towards the architecture and evolution of the buffalo and related genomes. Prospects of our present work in the context of comparative and functional genomics are highlighted.

Expressional dynamics of minisatellite 33.15 tagged spermatozoal transcriptome in Bubalus bubalis

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.