8 research outputs found
Genomics of the human Y chromosome and molecular diagnosis
No full textThe human Y chromosome carries a few functional genes as against a plethora of non-coding DNA sequences and shows a high degree of geographical and ethnic variations for a range of loci manifested as genetic polymorphisms. Y-chromosome linked sequence tagged sites (STS) and short tandem repeat (STR) marker systems offer infallible tool for gender identification, paternity testing, genome individualization and assessing male fertility status. Population-specific Y haplotypes and Single Nucleotide Polymorphisms (SNPs) are envisaged to be useful in establishing a correlation between diseased phenotypes with genetic polymorphisms. We discuss genomics of the human Y-chromosome and its possible applications in biology, medical and forensic sciences
Genomics of the human Y chromosome and molecular diagnosis
No full textThe human Y chromosome carries a few functional genes as against a plethora of non-coding DNA sequences and shows a high degree of geographical and ethnic variations for a range of loci manifested as genetic polymorphisms. Y-chromosome linked sequence tagged sites (STS) and short tandem repeat (STR) marker systems offer infallible tool for gender identification, paternity testing, genome individualization and assessing male fertility status. Population-specific Y haplotypes and Single Nucleotide Polymorphisms (SNPs) are envisaged to be useful in establishing a correlation between diseased phenotypes with genetic polymorphisms. We discuss genomics of the human Y-chromosome and its possible applications in biology, medical and forensic sciences
Characterization of a species-specific repetitive DNA from a highly endangered wild animal, Rhinoceros unicornis, and assessment of genetic polymorphism by microsatellite associated sequence amplification (MASA
Analysis of the evolutionarily conserved repeat motifs in the genome of the highly endangered central Indian swamp deer Cervus duvauceli branderi
No full textWe have analyzed the genome of central Indian swamp deer Cervus duvauceli branderi, an inhabitant of the Kanha National Park, a wildlife conservatory in Central India, with a view to provide a genetic basis for their extinction. Evolutionarily conserved repeat sequence motifs (GATA)3.75, TA(GATA)4, (GACA)3.75, (TGG)6 and a set of mouse β-actin primers were used to uncover the sequence variation within and between related species by employing techniques of hybridization and AP-PCR amplification. The oligo probe carrying the GACA and TGG repeat motifs was found to be positive with Cervus genome, whereas (GATA)3.75, TA(GATA)4 and β-actin probes did not cross-hybridize with the same. AP-PCR amplification with (GACA)3.75, unlike the (TGG)6 primer, generated distinct bands in the range of 0.37-2.10 kb amongst different genomes including Cervus. A comparative genome analysis of other species using the AP-PCR approach with (GACA)3.75 primer revealed the phylogenetic status of Cervus duvauceli branderi. From the analysis of a very limited number of Cervus DNA samples, we observed a high level of genetic homogeneity that may be a prime reason for the extinction of this species. This study has implications in the context of conservation of this endangered Cervus duvauceli branderi species
Characterization of a species-specific repetitive DNA from a highly endangered wild animal, Rhinoceros unicornis, and assessment of genetic polymorphism by microsatellite associated sequence amplification (MASA)
No full textWe have cloned and sequenced a 906 bp EcoRI repeat DNA fraction from Rhinoceros unicornis genome. The contig pSS(R)2 is AT rich with 340 A (37.53%), 187 C (20.64%), 173 G (19.09%) and 206 T (22.74%). The sequence contains MALT box, NF-E1, Poly-A signal, lariat consensus sequences, TATA box, translational initiation sequences and several stop codons. Translation of the contig showed seven different types of protein motifs, among which, EGF-like domain cysteine pattern signatures and Bowman-Birk serine protease inhibitor family signatures were prominent. The presence of eukaryotic transcriptional elements, protein signatures and analysis of subset sequences in the 5' region from 1 to 165 nt indicating coding potential (test code value=0.97) suggest possible regulatory and/or functional role(s) of these sequences in the rhino genome. Translation of the complementary strand from 906 to 706 nt and 190 to 2 nt showed proteins of more than 7 kDa rich in non-polar residues. This suggests that pSS(R)2 is either a part of, or adjacent to, a functional gene. The contig contains mostly non-consecutive simple repeat units from 2 to 17 nt with varying frequencies, of which four base motifs were found to be predominant. Zoo-blot hybridization revealed that pSS(R)2 sequences are unique to R. unicornis genome because they do not cross-hybridize, even with the genomic DNA of South African black rhino Diceros bicornis. Southern blot analysis of R. unicornis genomic DNA with pSS(R)2 and other synthetic oligo probes revealed a high level of genetic homogeneity, which was also substantiated by microsatellite associated sequence amplification (MASA). Owing to its uniqueness, the pSS(R)2 probe has a potential application in the area of conservation biology for unequivocal identification of horn or other body tissues of R. unicornis. The evolutionary aspect of this repeat fraction in the context of comparative genome analysis is discussed
