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DNA Barcoding in the Marine Habitat: An Overview

  • Subrata TrivediEmail author
  • Hasibur Rehman
  • Shalini Saggu
  • Chellasamy Panneerselvam
  • Zahid Khorshid Abbas
  • Iqbal Ahmad
  • Abid A. Ansari
  • Sankar K. Ghosh
Chapter

Abstract

Major part of our planet includes the marine habitat which faces severe threat due to overexploitation of its bio resources. Assessment of biodiversity in the massive and diverse marine ecosystem is a challenging task. In this introductory chapter, we give a brief description of the marine habitat and types of marine organisms, followed by the concept of DNA barcoding. We also describe the applications and different initiatives of DNA barcoding in the marine ecosystem. A brief account of DNA barcoding in marine fungi, different groups of animals and plants is also elucidated. This chapter gives a bird’s eye view on the DNA barcoding in the marine perspective.

Keywords

DNA barcoding Marine COI Biodiversity Conservation 

Notes

Acknowledgments

The authors gratefully acknowledge the Deanship of Scientific Research, University of Tabuk, Saudi Arabia, for the support provided through the projects numbered S-1434-0106, S-1435-0112 and S-1436-0252 to Dr. Subrata Trivedi (Principal Investigator).

References

  1. Ahmad I, Fatma Z, Yazdani SS (2013) DNA barcode and lipid analysis of new marine algae potential for biofuel. Algal Res 2:10–15. http://dx.doi.org/10.1016/j.algal.2012.10.003 Google Scholar
  2. Alfonsi E, Méheust E, Fuchs S (2013) The use of DNA barcoding to monitor the marine mammal biodiversity along the French Atlantic coast. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research. ZooKeys 365:5–24. http://dx.doi.org/10.3897/zookeys.365.5873
  3. Aliabadian M, Beentjes KK, Roselaar CS (2013) DNA barcoding of Dutch birds. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research. ZooKeys 365:25–48. http://dx.doi.org/10.3897/zookeys.365.6287
  4. Amin G, Biswas S, Zaman S, Pramanick P, Trivedi S, Mitra A (2015) Prediction of dissolved oxygen in Indian sundarbans: vision 2050. Int Adv Res J Sci Eng Technol 2(12):31–33CrossRefGoogle Scholar
  5. Andreakis N, Høj L, Kearns P, Hall MR, Ericson G, Cobb RE et al (2015) Diversity of marine-derived fungal cultures exposed by DNA barcodes: the algorithm matters. PLoS ONE 10(8):e0136130. doi: 10.1371/journal.pone.0136130 PubMedPubMedCentralCrossRefGoogle Scholar
  6. Ardura A, Planes S, Garcia-Vazquez E (2013) Applications of DNA barcoding to fish landings: authentication and diversity assessment. In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research. ZooKeys 365:49–65. http://dx.doi.org/10.3897/zookeys.365.6409
  7. Baldwin CC, Johnson GD (2014) Connectivity across the Caribbean sea: DNA barcoding and morphology unite an enigmatic fish larva from the Florida straits with a new species of sea bass from deep reefs off Curaçao. PLoS ONE 9(5):e97661. doi: 10.1371/journal.pone.0097661 PubMedPubMedCentralCrossRefGoogle Scholar
  8. Belinky F, Amir Szitenberg A, Goldfarb I, Feldstein T, Wörheide G, Ilan M, Huchon D (2012) ALG11—a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene. Mol Phylogenet Evol 63:702–713PubMedCrossRefGoogle Scholar
  9. Bhadury P, Austen MC, Bilton DT, Lambshead PJD, Rogers AD, Smerdon GR (2006) Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes. Mar Ecol Prog Ser 320:1–9CrossRefGoogle Scholar
  10. Bhattacharjee D, Samanta B, Danda AA (2013) Temporal succession of phytoplankton assemblages in a tidal creek system of the Sundarbans Mangroves: an integrated approach. Int J Biodiv. http://dxdoi.org/10.1155/2013/824543
  11. Blanco-Bercial L, Álvarez-Marqués F, Bucklin A (2011) Comparative phylogeography and connectivity of sibling species of the marine copepod Clausocalanus (Calanoida). J Exp Mar Biol Ecol 404:108–115CrossRefGoogle Scholar
  12. Blanco-Bercial L, Cornils A, Copley N, Bucklin A (2014) DNA barcoding of marine Copepods: assessment of analytical approaches to species identification. PLoS Curr 6. http://dx.doi.org/10.1371/currents.tol.cdf8b74881f87e3b01d56b43791626d2
  13. Böttger-Schnack R, Machida R (2011) Comparison of morphological and molecular traits for species identification and taxonomic grouping of oncaeid copepods. Hydrobiologia 666:111–125Google Scholar
  14. Briggs JC (1994) Species-diversity––land and sea compared. Syst Biol 43:130–135CrossRefGoogle Scholar
  15. Bucklin A, Frost BW (2009) Morphological and molecular phylogenetic analysis of evolutionary lineages within Clausocalanus (Copepoda: Calanoida). J Crust Biol 29:111–120CrossRefGoogle Scholar
  16. Bucklin A, Hopcroft RR, Kosobokova KN, Nigro LM, Ortman BD et al (2010a) DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition. Deep-Sea Res II 57:40–48Google Scholar
  17. Bucklin A, Ortman BD, Jennings RM, Nigro LM, Sweetman CJ et al (2010b) A ‘‘Rosetta Stone’’ for metazoan zooplankton: DNA barcode analysis of species diversity of the Sargasso Sea (Northwest Atlantic Ocean). Deep-Sea Res II 57:2234–2247Google Scholar
  18. Bucklin A, Steinke D, Blanco-Bercial L (2011) DNA barcoding of marine metazoa. Annu Rev Mar Sci 3:471–508. http://dx.doi.org/10.1146/annurev-marine-120308-080950 Google Scholar
  19. Cárdenas P, Menegola C, Rapp HT, Diaz MC (2009) Morphological description and DNA barcodes of shallow-water Tetractinellida (Porifera: Demospongiae) from Bocas del Toro, Panama, with description of a new species. Zootaxa 2276:1–39Google Scholar
  20. Carvalho FC, Pomponi SA, Xavier JR (2015) Lithistid sponges of the upper bathyal of Madeira, Selvagens and Canary Islands, with description of a new species of Isabella. J Mar Biol Assoc UK 95:1287–1296. doi: 10.1017/S0025315414001179 CrossRefGoogle Scholar
  21. Castellani C, Lindley AJ, Wootton M, Lee CM, Kirby RR (2012) Morphological and genetic variation in the North Atlantic copepod Centropages typicus. J Mar Biol Assoc UK 92:99–106Google Scholar
  22. Chinnappareddy LRD, Khandagale K, Reddy SHS, Chennareddy CKA, Singh TH (2012) SSR-based DNA barcodes as a tool for identification of eggplant genotypes. Int J Vegetable Sci 18(3):260–271. doi: 10.1080/19315260.2011.633976 CrossRefGoogle Scholar
  23. Clarkston BE, Saunders GW (2010) A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthoratim burtonii sp. Botany 88:119–131. http://dx.doi.org/10.1139/B09-101 Google Scholar
  24. Costa FO, Henzler CM, Lunt DH, Whiteley NM, Rock J (2009) Probing marine Gammarus (Amphipoda) taxonomy with DNA barcodes. Syst Biodivers 7(4):365–379. http://dx.doi.org/10.1017/S1477200009990120 Google Scholar
  25. Daru BH, Yessoufou K, Mankga LT, Davies TJ (2013) A global trend towards the loss of evolutionarily unique species in mangrove ecosystems. PLoS ONE 8(6):e66686. http://dx.doi.org/10.1371/journal.pone.0066686 Google Scholar
  26. De Wit P, Rota E, Erséus C (2009) Grania (Annelida: Clitellata: Enchytraeidae) of the Great Barrier Reef, Australia, including four new species and a re-description of Graniatrichaeta Jamieson, 1977. Zootaxa 2165:16–38Google Scholar
  27. Derycke S, Fonseca G, Vierstraete A, Vanfleteren J, Vincx M, Moens T (2008) Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morphological tools. Zool J Linn Soc 152:1–15CrossRefGoogle Scholar
  28. Dettai A, Lautredou AC, Bonillo C (2011) Theactinopterygian diversity of the CEAMARC cruises: barcoding and molecular taxonomy as a multi-level tool for new findings. Deep-Sea Res II 58(1):250–263CrossRefGoogle Scholar
  29. Dhaneesh KV, Kumar TTA, Kumar AB (2015) Barcoding, phylogeography and species boundaries in crownfishes of the Indian Ocean. DNA Barcodes 3:5–16Google Scholar
  30. Efe MA, Tavares ES, Baker AJ, Bonatto SL (2009) Multigene phylogeny and DNA barcoding indicate that the Sandwich tern complex (Thalasseussandvicensis, Laridae, Sternini) comprises two species. Mol Phylogenet Evol 52:263–267PubMedCrossRefGoogle Scholar
  31. Erpenbeck D, Hall K, Alvarez B, Büttner G, Sacher K, Schätzle S, Schuster A, Vargas S, Hooper JNA, Wörheide G (2012) The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data. Org Divers Evol 12:57–70. doi: 10.1007/s13127-011-0068-9 CrossRefGoogle Scholar
  32. Erpenbeck D, Ekins M, Enghuber N, Hooper JNA, Lehnert H, Poliseno A, Schuster A, Setiawan E, De Voogd NJ, Wörheide G, Soest RWM (2015) Nothing in (sponge) biology makes sense—except when based on holotypes. J Mar Biol Assoc UK. doi: 10.1017/S0025315415000521 Google Scholar
  33. Ghosh R, Trivedi S, Pramanick P, Zaman S, Mitra A (2015) Seagrass: a store house of carbon. J Energy Environ Carbon Credits 5(2):23–29Google Scholar
  34. Gray JS (1997) Marine biodiversity: patterns, threats and conservation needs. Biodiv Conserv 6:153–175CrossRefGoogle Scholar
  35. Hanner R, Becker S, Ivanova VN (2011) FISH-BOL and seafood identification: geographically dispersed case studies reveal systemic market substitution across Canada. Mitochondrial DNA 22(S1):106–122. http://dx.doi.org/10.3109/19401736.2011.588217 Google Scholar
  36. Hebert PD, Cywinska A, Ball SL (2003) Biological identifications through DNA barcodes. Proc Biol Sci R Soc 270(1512), 313–321. http://dx.doi.org/10.1098/rspb.2002.2218 Google Scholar
  37. Hirose M, Hirose E (2009) Barcoding in photosymbiotic species of Diplosoma (Ascidiacea: Didemnidae), with the description of a new species from the Southern Ryukyus Japan. Zool Sci 26(8):564–568. http://dx.doi.org/10.2108/zsj.26.564
  38. Holland LZ, Gibson-Brown JJ (2003) The Ciona intestinalis genome: when the constraints are off. BioEssays 25(6):529–532Google Scholar
  39. Holmes BH, Steinke D, Ward RD (2009) Identification of shark and ray fins using DNA barcoding. Fisher Res 95:280–288CrossRefGoogle Scholar
  40. Järnegren J, Schander C, Sneli J-A, Rønningen V, Young CM (2007) Four genes, morphology and ecology: distinguishing a newspecies of Acesta (Mollusca; Bivalvia) from the Gulf of Mexico. Mar Biol 152:43–55. http://dx.doi.org/10.1007/s00227-007-0651-y Google Scholar
  41. Jennings RM, Bucklin A, Ossenbrugger H, Hopcroft RR (2010a) Species diversity of planktonic gastropods (Pteropoda and Heteropoda) fromsix ocean regions based on DNA barcode analysis. Deep-Sea Res II 57:2199–2210. http://dx.doi.org/10.1016/j.dsr2.2010.09.022 Google Scholar
  42. Jennings RM, Bucklin A, Pierrot-Bults A (2010b) Barcoding of arrow worms (Phylum Chaetognatha) from three oceans: genetic diversity and evolution within an enigmatic phylum. PLoS ONE 5(4):e9949. http://dx.doi.org/10.1371/journal.pone.0009949 Google Scholar
  43. Joly S, Davies TJ, Archambault A, Bruaeau A, Derry A, Kembel SW, Peres–Neto P, Vamosi J, Wheeler TA (2013) Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour. doi: 10.1111/1755-0998.12173 PubMedGoogle Scholar
  44. Kamaruzzaman BY, John BA, Zaleha K, Jalal KCA (2011) Molecular phylogeny of horseshoe crab. Asian J Biotechnol 3:302–309CrossRefGoogle Scholar
  45. Kappner I, Bieler R (2006) Phylogeny of venus clams (Bivalvia: Venerinae) as inferred from nuclear and mitochondrial gene sequences. Mol Phylogenet Evol 40(2):317–331PubMedCrossRefGoogle Scholar
  46. Kemppainen P, Panova M, Hollander J, Johannesson K (2009) Complete lack of mitochondrial divergence between two species of NE Atlantic marine intertidal gastropods. J Evol Biol 22(10):2000–2011. http://dx.doi.org/10.1111/j.1420-9101.2009.01810.x Google Scholar
  47. Keshavmurthy S, Yang S-Y, Alamaru A, Chuang Y-Y, Pichon M, Obura D et al (2013) DNA barcoding reveals the coral ‘‘laboratory-rat’’, Stylophora pistillata encompasses multiple identities. Sci Rep 3:1520. doi: 10.1038/srep01520 PubMedPubMedCentralCrossRefGoogle Scholar
  48. Kim MS, Yang MY, Cho GY (2010) Applying DNA barcoding to Korean Gracilariaceae (Rhodophyta) Cryptogamie. Algologie 3(4):387–401Google Scholar
  49. Kochzius M, Seidel C, Antoniou A (2010) Identifying fishes through DNA barcodes and microarrays. PLoS ONE 5(9):e12620. http://dx.doi.org/10.1371/journal.pone.0012620 Google Scholar
  50. Kozol R, Blanco-Bercial L, Bucklin A (2012) Multi-Gene analysis reveals a lack of genetic divergence between Calanusagulhensis and C. sinicus (Copepoda; Calanoida). PLoS ONE 7:e45710Google Scholar
  51. Krug PJ, Ellingson RA, Burton R, Valdés A (2007) A new poecilogonous species of sea slug (Opisthobranchia: Sacoglossa) from California: comparison with the planktotrophiccongenermodesta (Lovén 1844). J Mollus Stud 73(1):29–38. doi: 10.1093/mollus/eyl025 CrossRefGoogle Scholar
  52. Laakmann S, Auel H, Kochzius M (2012) Evolution in the deep sea: biological traits, ecology and phylogenetics of pelagic copepods. Mol Phylogenet Evol 65:535–546PubMedCrossRefGoogle Scholar
  53. Lakra WS, Verma WS, Goswami M (2010) DNA barcoding Indian marine fishes. Mol Ecol Resour 11:60–71CrossRefGoogle Scholar
  54. Lavrov DV, Pett W, Voigt O, Wörheide G, Forget L, Franz Lang B, Kayaly E, (2012) Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): six linear chromosomes, fragmented rRNAs, tRNA Editing, and a novel genetic code. Mol Biol Evol 30(4):865–880. doi: 10.1093/molbev/mss274 Google Scholar
  55. Layton KKS, Martel AL, Hebert PDN (2014) Patterns of DNA barcode variation in canadian marine molluscs. PLoS ONE 9(4):e95003. http://dx.doi.org/10.1371/journal.pone.0095003 Google Scholar
  56. Lee G, Park SY, Hwang J, Lee Y-H, Hwang SY, Lee S, Lee T-K (2011) Development of DNA chip for jellyfish verification from South Korea. BioChip J 5(4):375–382. doi: 10.1007/s13206-011-5412-9 CrossRefGoogle Scholar
  57. Leray M, Knowlton N (2015) DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. PNAS 112(7):2076–2081PubMedPubMedCentralCrossRefGoogle Scholar
  58. Les DH, Moody ML, Jacobs SWL, Bayer RJ (2002) Systematics of seagrasses (Zosteraceae) in Australia and New Zealand. Syst Bot 27:468–484Google Scholar
  59. Li WY, Zhong J, Wang Y-Q (2010) Analysis of amphioxus geographic populations in the West Pacific Ocean based on COX Ι gene. Zool Res 31(4):375–380. doi: 10.3724/SP.J.1141.2010.04375 PubMedGoogle Scholar
  60. Lobo J, Teixeira MAL, Borges LMS, Ferreira MSG, Hollatz C, Gomes PT, Sousa R et al (2015) Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast. Mol Ecol Resour. doi: 10.1111/1755-0998.12441 PubMedGoogle Scholar
  61. Lowenstein JH, Amato G, Kolokotronis S-O (2009) The real maccoyii: identifying Tuna Sushi with DNA barcodes—contrasting characteristic attributes and genetic distances. PLoS ONE 4(11):e7866. http://dx.doi.org/10.1371/journal.pone.0007866 Google Scholar
  62. Lucas C, Thangaradjou T, Papenbrock J (2012) Development of a DNA barcoding systemforseagrasses: successful but not simple. PLoS ONE 7(1):e29987. doi: 10.1371/journal.pone.0029987 PubMedPubMedCentralCrossRefGoogle Scholar
  63. Maas AE, Blanco-Bercial L, Lawson GL (2013) Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding. PLoS ONE 8(1):e53889. http://dx.doi.org/10.1371/journal.pone.0053889 Google Scholar
  64. Mabragaña E, Díaz de Astarloa JM, Hanner R (2011) DNA barcoding identifies argentine fishes from marine and brackish waters. PLoS ONE 6(12):e28655. http://dx.doi.org/10.1371/journal.pone.0028655 Google Scholar
  65. Machida RJ, Tsuda A (2010) Dissimilarity of species and forms of planktonic Neocalanus copepods using mitochondrial COI, 12S, nuclear ITS, and 28S gene sequences. PLoS ONE 5(4):e10278. http://dx.doi.org/10.1371/journal.pone.0010278 Google Scholar
  66. Maturana CS, Rodrigo A, Moreno RA, Labra FA, González-Wevar CA, Rozbaczylo N, Carrasco FD, Poulin E (2011) DNA barcoding of marine polychaetes species of southern Patagonian fjords. Revista de Biología Marina y Oceanografía 46(1):35–42Google Scholar
  67. Mecklenburg CW, Moller PR, Steinke D (2011) Biodiversity of arctic marine fishes: taxonomy and zoogeography. Mar Biodiv 41:109–140CrossRefGoogle Scholar
  68. Mikkelsen NT, Schander C, Willassen E (2007) Local scale DNA barcoding of bivalves (Mollusca): a case study. Zool Scr 36(5):455–463. http://dx.doi.org/10.1111/j.1463-6409.2007.00289 Google Scholar
  69. Mitra A, Trivedi S, Zaman S, Pramanick P, Chakraborty S, Pal N, Fazli P, Banerjee K (2015) Decadal variation of nutrient level in two major estuaries in the Indian subdarbans. Jordan J Biol Sci 8(3):231–236Google Scholar
  70. Molnar JL, Gamboa RL, Revenga C (2008) Assessing the global threat of invasive species to marine biodiversity. Front Ecol Environ 6:485–492CrossRefGoogle Scholar
  71. Morrow CC, Picton BE, Erpenbeck D, Boury-Esnault N, Maggs CA, Allcock AL (2012) Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae). Mol Phylogenet Evol 62:174–190PubMedCrossRefGoogle Scholar
  72. Moura CJ, Harris DJ, Cunha MR, Rogers AD (2007) DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. Zool Scr 37(1):93–108. http://dx.doi.org/10.1111/j.1463-6409.2007.00312
  73. Nagy ZT, Sonet G, GlawF (2012) First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS ONE 7(3):e34506. http://dx.doi.org/10.1371/journal.pone.0034506 Google Scholar
  74. Naro-Maciel E, Reid B, Fitzsimmons NN (2009) DNA barcodes for globally threatened marine turtles: a registry approach to documenting biodiversity. Mol Ecol Resour 10:252–263. http://dx.doi.org/10.1111/j.1755-0998.2009.02747.x Google Scholar
  75. Park M-H, Sim C-J, Baek J, Min G-S (2007) Identification of genes suitable for DNA barcoding of morphologically indistinguishable Korean Halichondriidae sponges. Mol Cells 23(2):220–227PubMedGoogle Scholar
  76. Pauls SU, Blahnik RJ, Zhou X, Wardwell CT, Holzenthal RW (2010) DNA barcode data confirm new species and reveal cryptic diversityin Chilean Smicridea (Smicridea) (Trichoptera:Hydropsychidae). J N Am Benthol Soc 29(3):1058–1074. doi: 10.1899/09-108.1 Google Scholar
  77. Pires AC, Marinoni L (2010) DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies. Biota Neotrop 10(2)Google Scholar
  78. Plaisance L, Caley MJ, Brainard RE, Knowlton N (2011) The diversity of coral reefs: what are we missing? PLoS ONE 6(10):e25026. doi: 10.1371/journal.pone.0025026 PubMedPubMedCentralCrossRefGoogle Scholar
  79. Pöppe J, Sutcliffe P, Hooper JNA, Wörheide G, Erpenbeck D (2010) COI barcoding reveals new clades and radiation patterns of Indo-Pacific sponges of the family Irciniidae (Demospongiae: Dictyoceratida). PLoS ONE 5(4):e9950. doi: 10.1371/journal.pone.0009950 Google Scholar
  80. Puillandre N, Strong EE, Bouchet P (2009) Identifying gastropod spawn from DNA barcodes: possible but not yet practicable. Mol Ecol Resour 9:1311–1321. http://dx.doi.org/10.1111/j.1755-0998.2009.02576.x Google Scholar
  81. Raupach MJ, Barco A, Steinke D, Beermann J, Laakmann S, Mohrbeck I et al (2015) The application of DNA barcodes for the identification of marine crustaceans from the North Sea and adjacent regions. PLoS ONE 10(9):e0139421. doi: 10.1371/journal.pone.0139421 PubMedPubMedCentralCrossRefGoogle Scholar
  82. Razy-Krajka F, Lam K, Wang W, Stolfi A, Joly M, Bonneau R, Christiaen L (2014) Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors. Dev Cell 29(3):263–276. http://dx.doi.org/10.1016/j.devcel.2014.04.001 Google Scholar
  83. Satoh N, Satou Y, Davidson B, Levine M (2003) Ciona intestinalis: an emerging model for whole-genome analyses. Trends Genet 19(7):376–381PubMedCrossRefGoogle Scholar
  84. Schuster A, Erpenbeck D, Pisera A, Hooper J, Bryce M et al (2015) Deceptive desmas: molecular phylogenetics suggests a new classification and uncovers convergent evolution of lithistiddemosponges. PLoS ONE 10(1):e116038. doi: 10.1371/journal.pone.011603 PubMedPubMedCentralCrossRefGoogle Scholar
  85. Smith KF, Thia J, Gemmill CEC (2012) Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and provides a rapid method for Ciona species discrimination. Aquat Invasions 7(3): 305–313. http://dx.doi.org/10.3391/ai.2012.7.3.002 Google Scholar
  86. Sperling EA, Rosengarten RD, Moreno MA, Dellaporta SL (2012). The complete mitochondrial genome of the verongid sponge Aplysina cauliformis: implications for DNA barcoding in demosponges. Hydrobiologia 687:61–69 doi: 10.1007/s10750-011-0879-x Google Scholar
  87. Steinke D, Zemlak TS, Hebert PDN (2009) Barcoding Nemo: DNA-based identifications for the ornamental fish trade. PLoS ONE 4(7):e6300. http://dx.doi.org/10.1371/journal.pone.0006300 Google Scholar
  88. Stolfi A, Christiaen L (2012) Genetic and genomic toolbox of the chordate Ciona intestinalis. Genetics 192(1):55–66. http://dx.doi.org/10.1534/genetics.112.140590 Google Scholar
  89. Szitenberg A, Becking LE, Vargas S, Fernandez JCC, Santodomingo N, Wörheide G, Ilan M, Kelly M, Huchon D (2013) Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers. Mol Phylogenet Evol 67:509–519PubMedCrossRefGoogle Scholar
  90. Tack JF, Berghe E, Polk PH (1992) Ecomorphology of Crassostrea cucullata (Born, 1778) (Ostreidae) in a mangrove creek (Gazi, Kenya). Hydrobiologia 247:109–117CrossRefGoogle Scholar
  91. Tolkin T, Christiaen L (2012) Development and evolution of the ascidian cardiogenic mesoderm. Curr Top Dev Biol 100:107–142. http://dx.doi.org/10.1016/B978-0-12-387786-4.00011-7
  92. Trivedi S, Affan R, Alessa AHA et al (2014) DNA barcoding of Red Sea fishes from Saudi Arabia—the first approach. DNA Barcodes 2:17–20. http://dx.doi.org/10.2478/dna-2014-0003
  93. Trivedi S, Aloufi AA, Ansari AA, Ghosh SK (2015a) Molecular phylogeny of oysters belonging to the genus Crassostrea through DNA barcoding. J Entomol Zool Stud 3(1):21–26Google Scholar
  94. Trivedi S, Chakraborty S, Zaman S, Prosenjit P, Fazli P, Amin G, Mitra (2015b) Impact of salinity on the condition factor of commercially important Fin Fish in the lower Gangetic delta. J Environ Sci Comput Sci Eng Technol 4(2):473–480Google Scholar
  95. Trivedi S, Aloufi AA, Rehman H, Saggu S, Ghosh SK (2016a) DNA barcoding: tool for assessing species identification in reptilia. J Entomol Zool Stud 4(1):332–337Google Scholar
  96. Trivedi S, Aloufi AA, Ansari AA, Ghosh SK (2016b) Role of DNA barcoding in marine biodiversity assessment and conservation: an update. Saudi J Biol Sci. http://dx.doi.org/10.1016/j.sjbs.2015.01.00
  97. Trivedi S, Ansari AA, Rehman H, Saggu S, Abbas ZK, Ghosh SK (2016c) DNA barcoding as a molecular tool for the assessment of plant biodiversity. In: Ansari AA, Gill SS (eds) Plant biodiversity: monitoring assessment and conservation. CABI Publications, Wallingford (In press)Google Scholar
  98. Trivedi S, Ueki T, Yamaguchi N, Michibata H (2003) Novel Vanadium-binding proteins (vanabins) identified in cDNA libraries and the genome of the ascidian Ciona intestinalis. Biochim Biophys Acta 1630:64–70PubMedCrossRefGoogle Scholar
  99. Uchimura M, Faye EJ, Shimada S, Inoue T, Nakamura Y (2008) A reassessment of Halophila species (Hydrocharitaceae) diversity with special reference to Japanese representatives. Bot Mar 51:258–268CrossRefGoogle Scholar
  100. Uthicke S, Byrne M, Conand C (2010) Genetic barcoding of commercial Bêche-de-mer species (Echinodermata: Holothuroidea). Mol Ecol Resour 10(4)–646. http://dx.doi.org/10.1111/j.1755-0998.2009.02826.x Google Scholar
  101. Vanhove MPM, Tessens B, Schoelinck C, Jondelius U, Littlewood DTJ, Artois T, Huyse T (2013) Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes). In: Nagy ZT, Backeljau T, De Meyer M, Jordaens K (eds) DNA barcoding: a practical tool for fundamental and applied biodiversity research. ZooKeys 365:355–379. doi: 10.3897/zookeys.365.5776 Google Scholar
  102. Vargas S, Erpenbeck D, Göcke C, Hall KA, Hooper JNA, Janussen D, Wörheide G (2013). Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sponges. ZoologicaScripta 42:106–116Google Scholar
  103. Vargas S, Kelly M, Schnabel K, Mills S, Bowden D, Wörheide G (2015) Diversity in a cold hot-spot: DNA-barcoding reveals patterns of evolution among Antarctic demosponges (Class Demospongiae, Phylum Porifera). PLoS ONE 10(6):e0127573. doi: 10.1371/journal.pone.0127573 PubMedPubMedCentralCrossRefGoogle Scholar
  104. Vargas S, Schuster A, Sacher K, Büttner G, Schätzle S et al (2012) Barcoding sponges: an overview based on comprehensive sampling. PLoS ONE 7(7):e39345. doi: 10.1371/journal.pone.003934 PubMedPubMedCentralCrossRefGoogle Scholar
  105. Vargas SM, Araújo FCF, Santos FR (2009) DNA barcoding of Brazilian sea turtles (Testudines). Genet Mol Biol 32(3):608–612PubMedPubMedCentralCrossRefGoogle Scholar
  106. Velmurugan S, Prasannakumar C, Manokaran S, Ajithkumar T, Samkamaleson A, Palavesam A (2013) DNA barcodes for marine fungal identification and discovery. Fungal Ecol 6:408–418. http://dx.doi.org/10.1016/j.funeco.2013.05.003 Google Scholar
  107. Vences M, Thomas M, Meijden A, Chiari Y, Vieites DR (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2:5. doi: 10.1186/1742-9994-2-5 PubMedPubMedCentralCrossRefGoogle Scholar
  108. Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes. J Fish Biol 74:329–356PubMedCrossRefGoogle Scholar
  109. Ward RD, Holmes BH, O’hara TD (2008) DNA barcoding discriminates echinoderm species. Mol Ecol Resour 8(6):1202–1211PubMedCrossRefGoogle Scholar
  110. Ward RD, Zemlak TS, Innes BH (2005) Barcoding Australia’s fish species. Phil Trans R Soc Lond B 360:1847–1857CrossRefGoogle Scholar
  111. Waycott M, Duarte CM, Carruthers TJB et al (2009) Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proc Natl Acad Sci USA 106:12377–12381PubMedPubMedCentralCrossRefGoogle Scholar
  112. Waycott M, Freshwater DW, York RA et al (2002) Evolutionary trends in the seagrass genus Halophila (thouars): Insights from molecular phylogeny. Bull Mar Sci 71:1299–1308Google Scholar
  113. Weigt LA, Baldwin CC, Driskell A (2012) Using DNA barcoding to assess Caribbean Reef fish biodiversity: expanding taxonomic and geographic coverage. PLoS ONE 7(7):e41059. http://dx.doi.org/10.1371/journal.pone.0041059 Google Scholar
  114. Wörheide G, Erpenbeck D, Menke C (2007) The sponge barcoding project: aiding in the identification and description of poriferan taxa. Porifera Res Biodivers Innov Sustain 2007:123–128Google Scholar
  115. Xiaobo Z, Shaojun P, Tifeng S (2013) Applications of three DNA barcodes in assorting intertidal red Macroalgal Flora in Qingdao, China. J Ocean Univ China 12(1):139–145. http://dx.doi.org/10.1007/s11802-013-2052-9
  116. Zemlak TS, Ward RD, Connell AD (2009) DNA barcoding reveals overlooked marine fishes. Mol Ecol Resour 9(1):237–242. http://dx.doi.org/10.1111/j.1755-0998.2009.02649.x Google Scholar
  117. Zhang H, Zhang Y, Zhang Z, Gao T (2013) DNA barcodes of eight species in genus Sebastes. Biochem Syst Ecol 48:45–50. http://dx.doi.org/10.1016/j.bse.2012.11.012 Google Scholar
  118. Zhang J (2011) Species identification of marine fishes in China with DNA barcoding. Evid Based Complement Altern Med. Article ID 978253, 10p. http://dx.doi.org/10.1155/2011/978253
  119. Zhang J-B, Hanner R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol 39:31–42CrossRefGoogle Scholar
  120. Zhou H, Zhang Z, Chen H, Sun R, Wang H, Guo L, Pan H (2010) Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China. Chin J Oceanol Limnol 28(4):899–910. doi: 10.1007/s00343-010-9131-1 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Subrata Trivedi
    • 1
    Email author
  • Hasibur Rehman
    • 1
  • Shalini Saggu
    • 1
  • Chellasamy Panneerselvam
    • 1
  • Zahid Khorshid Abbas
    • 1
  • Iqbal Ahmad
    • 2
  • Abid A. Ansari
    • 1
  • Sankar K. Ghosh
    • 3
  1. 1.Faculty of Sciences, Department of BiologyUniversity of TabukTabukSaudi Arabia
  2. 2.Center for Environmental and Marine StudiesUniversity of AveiroAveiroPortugal
  3. 3.Department of BiotechnologyAssam UniversitySilcharIndia

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