Fingerprint: Visual description of variation in multiple sequence alignments of intra-species of rice genotypes belonging to Chhattisgarh

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.