International Journal of Chemical Studies
Vol. 6, Issue 1 (2018)
Fingerprint: Visual description of variation in multiple sequence alignments of intra-species of rice genotypes belonging to Chhattisgarh
Author(s): Jyoti Singh, Datta P Kakade and Shubha Banerjee
Abstract: The usefulness of genetic material for use as DNA barcodes is under stable evolution and advancement as new barcodes offering better resolution and efficiency of amplification for specific species groups are identified. The panel of 24 rice genotypes including diverse germplasm lines, elite lines, landraces and wild rice belonging to Chhattisgarh were amplified using atpH-atpI, petA-psbJ, trnK, rbcL, matK, trnlc-trnld, psbA-trnH aligned sets of seven chloroplast specific loci, sequences were analyzed using fingerprint available at http://evol.mcmaster.ca/fingerprint. Fingerprint helps to identify similarities, differences, and patterns within a multiple sequence alignment which is biologically valuable because it permits visualization of the distribution of a particular feature and inferences about the structure, function, and evolution of the sequences in analysis also represent identity, variability, charge, hydrophobicity, solvent accessibility, and structure along with new visualizations based on composition, heterogeneity, heterozygosity, dN/dS and nucleotide diversity. The visualization based on composition, heterogeneity, dN/dS and nucleotide diversity on 24 were performed. The results shows even though matK and rbcl loci shows lesser number of haplotypes but are variable throughout the region. On the other part psbA-trnH shows variability in the specific region through showed good discrimination power in molecular phylogenetic analysis.
Pages: 686-690 | 345 Views 10 Downloads
How to cite this article:
Jyoti Singh, Datta P Kakade, Shubha Banerjee. Fingerprint: Visual description of variation in multiple sequence alignments of intra-species of rice genotypes belonging to Chhattisgarh. Int J Chem Stud 2018;6(1):686-690.