Mitochondrial DNA diversity: Insight into population diversity, structure and demographic history ofPenaeus monodonalong the entire coastal region of India

The giant black tiger shrimp,Penaeus monodon, is one of the most economically important marine shrimp species, and it has a huge global economic impact. In this study, population diversity ofP. monodonalong the nine distinct coastal regions of India was determined by the molecular data of the mitochondrial control region (D-Loop) and five mitochondrial genes (12SrRNA, 16SrRNA, COX1, Cytb and ND1). The mitochondrial DNA regions were highly AT-rich, and demographic events suggested a recent population expansion. The results revealed a high level of genetic diversity, and we observed an increment of rare mutations and haplotypes within all populations. Chennai and Port Blair population showed the highest number of unique haplotypes. A significant level of population differentiation existed within all populations. A high level of genetic variations was observed within all populations. Neutral point mutations (silent or missense) were observed within all mitochondrial protein-coding genes. The mitochondrial control region (D-Loop), 16S ribosomal RNA and cytochrome b gene should be the potential marker forP. monodon. The 16S ribosomal RNA region would be the best mitochondrial marker for biogeographical phylogenetic studies inP. monodon. This study might have a great significance for the establishment of selective breeding strategies to develop genetically improved broodstock and to maintain wild stock diversity.