Indian Journal of Biotechnology Vol 15, April 2016, pp 172-177 Nuclear and mitochondrial DNA markers based identification of blunthorn lobster Palinustus waguensis Kubo, 1963 from South-west coast of India Rekha Devi Chakraborty*, G Maheswarudu, P Purushothaman, G Kuberan, Jomon Sebastian, E V Radhakrishnan and R Thangaraja Crustacean Fisheries Division, ICAR-Central Marine Fisheries Research Institute (CMFRI) Ernakulam North PO Cochin 682 018, India Received 14 December 2014; revised 3 April 2015; accepted 20 May 2015 The present study reports the occurrence of Palinustus waguensis Kubo, 1963 from South-west coast of India on the basis of morphological as well as molecular data. The DNA sequences of two mitochondrial genes, large subunit ribosomal DNA (16S rDNA) and cytochrome oxidase I (COI), and two nuclear-protein coding genes, viz., phosphoenolpyruvate carboxykinase (PEPCK) and sodium-potassium ATPase α-subunit (NaK), were submitted in the GenBank. Morphological examination of the specimen confirmed the identity of the species as P. waguensis. The pairwise genetic distance analysis, sequence identity and phylogenetic tree have shown that the specimen has similarity only with 16S rDNA sequence of P. waguensis of earlier reports. In the case of other genetic markers, it has shown some identity towards P. unicornutus and P. holthuisi, but with a high genetic difference. This study with sequence data of P. waguensis in GenBank will help to identify the specimen on molecular basis in future. Keywords: Blunthorn lobster (Palinustus waguensis), deepsea, genetic markers, phylogenetics, taxonomy Introduction Palinustus waguensis Kubo, 1963 is a deepsea blunthorn lobster belonging to the group of spiny lobsters 1 . It is a rare species living on rocky habitats and deep reef slopes of a depth range of 100-200 m 2,3 . It has both edible as well as ornamental value. Five species that have been described in this genus are P. holthuisi Chan and Yu, 1995, P. mossambicus Barnard, 1926, P. truncates A. Milne-Edwards, 1880, P. unicornutus Berry, 1979, and P. waguensis Kubo, 1963 with their occurrence seem to be very scarce and all occur at considerable depths. The two earlier reports of landing of P. waguensis from Indian waters are from Kasimedu, Chennai and Cuddalore 4,5 . The taxonomic status of some of the species still has to be proven by study of extensive material in depth. Mitochondrial and nuclear DNA markers are increasingly used in population and phylogenetic studies of organisms. The large subunit ribosomal DNA (16S rDNA) and cytochrome oxidase I (COI) genes, the slowest evolving genes in the mitochondrial genome, are used as markers for species-specific identification in many fishes 6,7 . Since mitochondrial DNA is maternally inherited, the phylogenies derived from mitochondrial DNA data may not provide the entire picture of the evolutionary relationship 8 . Hence, two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase (PEPCK) and sodium-potassium ATPase α-subunit (NaK) are currently being used as efficient molecular markers for phylogenetic studies 9 . These four DNA markers are successfully used to detect genetic uniqueness of individuals, populations or species 10-13 . They provide precise knowledge on phylogenetic relationships and resolve taxonomic ambiguities 14-17 . Specific DNA regions on nuclear and mitochondrial genome as novel biological information markers combined with existing morphological characters can provide reliable taxonomic information required for species identification 18 . The present study was undertaken to sequence two mitochondrial genes, 16S rDNA and COI, and two nuclear genes, PEPCK and NaK of P. waguensis landed in trawls off Sakthikulangara from South-west coast of India. Based on these sequences, genetic variations, sequence identity and phylogenetic relationship of the specimen with other closely related —————— *Author for correspondence: Tel: + 91-484-2394867; Fax : + 91-484-2394909 rekhadevi76@yahoo.com