Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA

• Published in: Meta Gene 2016-02, Vol.7, p.56-63
• Main Authors: Kehie, Mechuselie, Kumaria, Suman, Devi, Khumuckcham Sangeeta, Tandon, Pramod
• Format: Article
• Language: English
• Subjects: Haplotype; Naga King Chili; Nucleotide diversity; Phylogenetic; Sequence analysis
• ISSN: 2214-5400; 2214-5400
• DOI: 10.1016/j.mgene.2015.11.006

Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift–mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili. •The phylogenetic relationship of Naga King Chili showed a clear grouping from C. chinense and C. frutescens.•Naga King Chili population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure.•Our findings revealed an ancient evolutionary history of this species.