Molecular phylogeny of Shrimps from west coast of Maharashtra using DNA barcoding
Keywords:
COI gene, DNA Barcoding, shrimp, 16S rRNAAbstract
Crustaceans represent metazoan group with enormous morphological and ecological diversity but are difficult to identify with traditional approaches and require help of expert taxonomists. DNA barcoding technique is the most reliable molecular approach of species identification and provides permanent species tags. In case of crustaceans, sequence of two mitochondria genes COI and 16S rRNA have been found useful for correlation between taxonomic ranks and molecular divergence. Parapenaeopsis stylifera, Solenocera crassicornis and Fenneropenaeus indicus among penaeids and Nematopalaemon tenuipes, Exhippolysmata ensirostris & Acetes indicus considered as non-penaeids representing 5 families were collected from Mumbai, the major fishing region in Maharashtra. DNA barcode and Accession numbers were generated for these species. Molecular phylogenetic evolutionary study was carried out to evaluate genetic divergence between species with respect to their families and based on protein coding COI and non-protein coding 16S genes.
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Bilgin R, Utkan MA, Kalkan E, Karhan SU and Bekbölet M (2014) DNA barcoding of twelve shrimp species (Crustacea: Decapoda) from Turkish seas reveals cryptic diversity. Mediterranean Marine Science, 16(1), 36–45.
Carvalho Daniel C, Neto DA, Brasil BS, and Oliveira DA (2011) DNA barcoding unveils a high rate of mislabeling in a commercial freshwater catfish from Brazil. Mitochondrial DNA, 22(sup1), 97–105.
Carvalho Daniel Cardoso, Palhares RM, Drummond MG and Frigo, TB (2015) DNA Barcoding identification of commercialized seafood in South Brazil: A governmental regulatory forensic program. Food Control, 50, 784–788.
Crandall KA, Fetzner Jr, JW, Lawler SH, Kinnersley M and Austin C. M (1999) Phylogenetic relationships among the Australian and New Zealand genera of freshwater crayfishes (Decapoda: Parastacidae). Australian Journal of Zoology, 47(2), 199-.
Daniels SR, Hamer M, and Rogers C (2004) Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca): RADIATION OF STREPTOCEPHALUS. Biological Journal of the Linnean Society, 82(3), 313–327.
De Grave S, Li CP, Tsang LM, Chu KH and Chan TY (2014) Unweaving hippolytoid systematics (Crustacea, Decapoda, Hippolytidae): Resurrection of several families. Zoologica Scripta, 43(5), 496–507.
Deshmukh VD (1994). The non-penaeid prawn resources. Marine Fisheries Information Service, Technical and Extension Series, 130, 5–8.
Deshmukh VD (2004). Non-penaeid prawns.
Drumm D, Canino M, Buckley T and Paquin M (n.d.). DNA Barcoding Analysis of Marine Caridean Shrimps from Alaska.
Fischer W and Bianchi G (1984) FAO species identification sheets for fishery purposes: Western Indian Ocean (Fishing Area 51). V. 1: Introductory material. Bony fishes, families: Acanthuridae to Clupeidae.-v. 2: Bony fishes, families: Congiopodidae to Lophotidae.-v. 3:... Families: Lutjanidae to Scaridae.-v. 4:... Families: Scatophagidae to Trichiuridae.-v. 5: Bony fishes, families: Triglidae to Zeidae. Chimaeras. Sharks. Lobsters. Shrimps and prawns. Sea turtles. V. 6: Alphabetical index of scientific names and vernacular names.
Hebert PDN, Cywinska A, Ball SL and deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313–321.
Hebert PDN, Stoeckle MY, Zemlak TS and Francis CM (2004) Identification of Birds through DNA Barcodes. PLoS Biology, 2(10), e312.
Hurzaid A, Chan TY, Mohd Nor SA, Muchlisin ZA, and Chen WJ (2020) Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South‐East Asian waters. Zoologica Scripta, 49(5), 596-613.
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111–120.
Katneni VK, Shekhar MS, Jangam AK, Paran BC, Selvaraj A, Krishnan K, et al. (2021) Phylogenetic relations and mitogenome‐wide similarity metrics reveal monophyly of Penaeus sensu lato. Ecology and evolution, 11(5), 2040-2049.
Kumar S, Stecher G and Tamura K (2016) MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874.
Lavery S, Chan TY, Tam YK and Chu KH (2004) Phylogenetic relationships and evolutionary history of the shrimp genus Penaeus s.l. Derived from mitochondrial DNA. Molecular Phylogenetics and Evolution, 31(1), 39–49.
Machado EG, Dennebouy N, Suarez MO, Mounolou JC, and Monnerot M (1993) Mitochondrial 16s-Rrna Gene of Two Species of Shrimps: Sequence Variability and Secondary Structure. Crustaceana, 65(3), 279–286. JSTOR.
Multalin interface page. (n.d.). Retrieved March 1, 2019, from http://multalin.toulouse.inra.fr/multalin/
Munasinghe DHN, Murphy NP and Austin CM (2003) Utility of Mitochondrial DNA Sequences from Four Gene Regions for Systematic Studies of Australian Freshwater Crayfish of the Genus Cherax (Decapoda: Parastacidae). Journal of Crustacean Biology, 23(2), 402–417.
Murphy NP and Austin CM (2002) A preliminary study of 16S rRNA sequence variation in Australian Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in nitheir current classification. Invertebrate Systematics, 16(5), 697.
Murphy, Nicholas P and Austin CM (2003) Molecular taxonomy and phylogenetics of some species of australian palaemonid shrimps. Journal of Crustacean Biology, 23(1), 9.
Murphy Nicholas P and Austin CM (2004) Multiple origins of the endemic Australian Macrobrachium (Decapoda: Palaemonidae) based on 16S rRNA mitochondrial sequences. Australian Journal of Zoology, 52(5), 549.
Murray BW, McClymont RA and Strobeck, C. (1995). Forensic identification of ungulate species using restriction digests of PCR-amplified mitochondrial DNA. Journal of Forensic Sciences, 40(6), 943–951.
Palumbi SR, and Benzie, J. (1991). Large mitochondrial DNA differences between morphologically similar penaeid shrimp. Molecular Marine Biology and Biotechnology, 1(1), 27–34.
Quan J, Zhuang Z, Deng J, Dai J and Zhang Y (2004) Phylogenetic Relationships of 12 Penaeoidea Shrimp Species Deduced from Mitochondrial DNA Sequences. Biochemical Genetics, 42(9/10), 331–345.
Rajkumar G, Bhavan PS, Udayasuriyan R and Vadivalagan C (n.d.). Molecular identification of shrimp species, Penaeus semisulcatus, Metapenaeus dobsoni, Metapenaeus brevicornis, Fenneropenaeus indicus, Parapenaeopsis stylifera and Solenocera crassicornis inhabiting in the coromandel coast (Tamil Nadu, India) using MT-COI gene. 11.
Righting the Wrongs: Structural Insights into Replicating Damaged DNA. (2006). PLoS Biology, 4(1), e32.
Samadi S, Ghavam Mostafavi P, Rezvani Gilkolaii S, Fatemi M, and Fazli H (2016) Phylogenetic relationships of the commercial marine shrimp family Penaeidae from Persian Gulf. Iranian Journal of Fisheries Sciences, 15(1), 333-346.
Savolainen V, Cowan RS, Vogler AP, Roderick GK and Lane R (2005) Towards writing the encyclopaedia of life: An introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1805–1811.
Smith MA, Woodley NE, Janzen DH, Hallwachs W and Hebert PDN (2006) DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the United States of America, 103(10), 3657.
Waed, AR, Carrero JC, Garcia-Varela M, Gracia A and Laclette JP (2004) Molecular phylogeny of Superfamily Penaeoidea Rafinesque-Schmaltz, 1815, based on mitochondrial 16S partial sequence analysis. Journal of Shellfish Research, 23(3), 911-. Academic OneFile.
Voloch CM, Freire PR and Russo CAM (n.d.). Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae). 13.
Voloch CM, Freire PR, and Russo CAM (2005) Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers. Genetics and Molecular Research, 7.
Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol, 3(5), 294–299.
Ward RD, Zemlak TS, Innes BH, Last PR and Hebert P DN (2005) DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1847–1857.
Wu F, Li M, Liao B, Shi X, and Xu Y (2019) DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China. Forests, 10(1), 56.
Xiong J (2006) Essential Bioinformatics. Cambridge University Press. https://doi.org/10.1017/CBO9780511806087.
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