Molecular characterization of major and minor rDNA repeats and genetic variability assessment in different species of mahseer found in North India

Abstract

Relationship among the mahseer species (Family: Cyprinidae) has long been debated in fish systematics. Present study concentrates on the nature of the phylogenetic relationship among the five mahseer species using the sequence of major ribosomal DNA (45S rDNA). We have covered rDNA sequence of approximately 5.2 kb per individual, 26.0 kb per species and 130.0 kb as a whole. We also characterized the 45S and 5S rDNA regions with respect to their nucleotide composition. For phylogenetic analyses, nucleotide sequences were divided into four datasets. First and second datasets contained 18S rDNA and ITS1 sequence, whereas third and fourth datasets consisted of ITS2 and complete 18S-ITS1-5.8S-ITS2-28S, respectively. The NJ tree was constructed for all the datasets. The mahseer species under study formed a monophyletic group well separated from the outgroup species. Similarly, the individuals of Neolissochilus hexagonolepis form monophyletic group with Tor species, indicating Neolissochilus as a sister genus of Tor. The findings from the present study provide greater insights into taxonomic status of mahseer, and set the stage for future investigations dealing with phylo-geography, taxonomy, conservation and co-evolution within this interesting and important group of fish.

Keywords: 5-bromo-4-chloro-3′-indolyphosphate p-toluidine salt; AIC; AgNO(3); Akaike Information Criterion; BCIP; CMA(3); Chromomycin A(3); DNA; EMBL; European Molecular Biology Laboratory; FISH; IE; ITS1; ITS2; KCl; Magnesium chloride; Mahseers; MgCl(2); NBT; NCBI; NH; NJ; NTS; National Center for Biotechnology Information; Neolissochilus; Neolissochilus hexagonolepis; Non-transcribed spacer; PCR; Phylogeny; Potassium chloride; SM; TC; TP; TPr; TT; Tor; Tor chelynoides; Tor progeneius; Tor putitora; Tor tor; Tris hydrochloride; Tris–HCl; dNTPs; deoxynucleoside triphosphates; deoxyribonucleic acid; fluorescence in situ hybridization; intermediate element; internal transcribed spacer 1; internal transcribed spacer 2; neighbor-joining; nitro-blue tetrazolium chloride; polymerase chain reaction; rDNA; ribosomal deoxyribonucleic acid; silver nitrate; supplementary materials.