Published January 24, 2022 | Version v1
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Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori

  • 1. Zoology Department, Faculty of Science, Menoufia University, Menoufia, Egypt
  • 2. National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt
  • 3. National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt & hamdy_nfra@yahoo.com; https://orcid.org/0000-0002-4684-0473
  • 4. Minori Co. Ltd, Tako-machi, Chiba, Japan. mohammad_mongoose2007@yahoo.com; https://orcid.org/0000-0001-8106-5233 emanabbas03@yahoo.com; https://orcid.org/0000-0002-1716-025X
  • 5. National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt & elsayed_pin@yahoo.com; https://orcid.org/0000-0003-2647-4370
  • 6. National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt & fatma_abdelrazek@hotmail.com; https://orcid.org/0000-0002-8568-2324
  • 7. National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt & tahasoliman2000@gmail.com; https://orcid.org/0000-0003-3185-3092

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Mohammed-Geba, Khaled, Abbas, Eman M., Ahmed, Hamdy O., Shalabi, Mohammed A., Hamed, El Sayed A. E., Abdel Razek, Fatma A., Soliman, Taha (2022): Comparing genetic markers' efficiencies for discrimination between two commercially important holothuroids in the Mediterranean Sea, Holothuria polii and Holothuria sanctori. Zootaxa 5092 (5): 559-575, DOI: 10.11646/zootaxa.5092.5.4

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  • Ahmed, M.I. (2016) Induced spawning in the sea cucumber Holothuria atra from the Egyptian coast of the Red Sea. Egyptian Journal of Aquatic Biology and Fisheries, 20 (4), 9-15. https://doi.org/10.21608/ejabf.2016.11173
  • Ahmed, Q., Ali, Q.M. & Macdonald, A.H. (2021) Identification of Sea cucumber Holothuria (Lessonothuria) pardalis (Selenka, 1867) and Holothuria (Semperothuria) cinerascens (Brandt, 1835) (Family-Holothuriidae) based on morphological and mitochondrial DNA evidence and phylogenetic analysis from Karachi Coast, Pakistan. International Journal of Environment and Geoinformatics, 8 (1), 57-64. https://doi.org/10.30897/ijegeo.820617
  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215 (3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  • Arndt, A., Marquez, C., Lambert, P. & Smith, M.J. (1996) Molecular Phylogeny of Eastern Pacific Sea Cucumbers (Echinodermata: Holothuroidea) Based on Mitochondrial DNA Sequence. Molecular Phylogenetic and Evolution, 6, 425-437. https://doi.org/10.1006/mpev.1996.0091
  • Aydin, M. (2016) Sea cucumber (Holothuroidea) species of Turkey. Turk Denizcilik ve Deniz Bilimleri Dergisi, 2 (1), 49-58.
  • Bordbar, S., Anwar, F. & Saari, N. (2011) High-Value Components and Bioactives from Sea Cucumbers for Functional Foods-A Review. Marine Drugs, 9 (10), 1761-1805. https://doi.org/10.3390/md9101761
  • Borrero-Perez, G.H., Perez-Ruzafa, A., Marcos, C. & Gonzalez-Wangueemert, M. (2009) The taxonomic status of some Atlanto-Mediterranean species in the subgenus Holothuria (Echinodermata: Holothuroidea: Holothuriidae) based on molecular evidence. Zoological Journal of the Linnean Society, 157 (1), 51-69. https://doi.org/10.1111/j.1096-3642.2009.00529.x
  • Borrero-Perez, G.H., Gomez-Zurita, J., Gonzalez-Wanguemert, M., Marcos, C. & Perez-Ruzafa, A. (2010) Molecular systematics of the genus Holothuria in the Mediterranean and Northeastern Atlantic and a molecular clock for the diversification of the Holothuriidae (Echinodermata: Holothuroidea). Molecular Phylogenetics and Evolution, 57 (2), 899-906. https://doi.org/10.1016/j.ympev.2010.08.019
  • Borrero-Perez, G.H. & Vanegas-Gonzalez, M.J. (2019) Holothuria (Mertensiothuria) viridiaurantia sp. nov. (Holothuriida, Holothuriidae), a new sea cucumber from the Eastern Pacific Ocean revealed by morphology and DNA barcoding. ZooKeys, 893, 1-19. https://doi.org/10.3897/zookeys.893.36013
  • Bronstein, O. & Kroh, A. (2019) The first mitochondrial genome of the model echinoid Lytechinus variegatus and insights into Odontophoran phylogenetics. Genomics, 111 (4), 710-718. https://doi.org/10.1016/j.ygeno.2018.04.008
  • Bronstein, O., Kroh, A. & Haring, E. (2016) Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes). Molecular Phylogenetics and Evolution, 104, 1-13. https://doi.org/10.1016/j.ympev.2016.07.028
  • Byrne, M., Rowe, F. & Uthicke, S. (2010) Molecular taxonomy, phylogeny and evolution in the family Stichopodidae (Aspidochirotida: Holothuroidea) based on COI and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution, 56 (3), 1068-1081. https://doi.org/10.1016/j.ympev.2010.04.013
  • Clouse, R., Janies, D. & Kerr, A.M. (2005) Resurrection of Bohadschia bivittata from B. marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence. Zoology, 108 (1), 27-39. https://doi.org/10.1016/j.zool.2004.07.007
  • Colgan, D.J., McLauchlan, A., Wilson, G.D.F., Livingston, S.P., Edgecombe, G.D., Macaranas, J., Cassis, G. & Gray, M.R. (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Australian Journal of Zoology, 46 (5), 419-437. https://doi.org/10.1071/ZO98048
  • Conand, C. (1996) Asexual reproduction by fission in Holothuria atra: Variability of some parameters in populations from the tropical Indo-Pacific. Oceanologica Acta, 19 (3-4), 209-216.
  • Dafni, J. (1983) A new subspecies of Tripneustes gratilla from the northern Red Sea (Echinodermata: Echinoidea: Toxopneustidae). Israel Journal of Ecology and Evolution, 32 (1), 1-12.
  • Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9 (8), 772. https://doi.org/10.1038/nmeth.2109
  • Dolmatov, I.Y. (2014) New data on asexual reproduction, autotomy, and regeneration in holothurians of the Order Dendrochirotida. Russian Journal of Marine Biology, 40 (3), 228-232. https://doi.org/10.1134/S1063074014030031
  • Dupont, S., Ortega-Martinez, O. & Thorndyke, M. (2010) Impact of near-future ocean acidification on echinoderms. Ecotoxicology, 19 (3), 449-462. https://doi.org/10.1007/s10646-010-0463-6
  • Fernandes, T.J.R., Amaral, J.S. & Mafra, I. (2020) DNA barcode markers applied to seafood authentication: an updated review. Critical Reviews in Food Science and Nutrition, 61 (22), 3904-3935. https://doi.org/10.1080/10408398.2020.1811200
  • Fisher, W., Schneider, M. & Bauchot, M.L. (1987) Guide FAO d'Identification des Especes pour les Besoins de la Peche Mediterranee et Mer Noire - Zone de Peche 37, Vol. 1. Vegetaux et Invertebres. Organisation des Nations Unies pour l'Alimentation et l'Agriculture. Available from: http://www.fao.org/docrep/009/x0170f/x0170f00.htm (accessed October 2021)
  • Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294-299.
  • Funk, D.J. & Omland, K.E. (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology, Evolution, and Systematics, 34 (1), 397-423. https://doi.org/10.1146/annurev.ecolsys.34.011802.132421
  • Galal-Khallaf, A., Ardura, A., Mohammed-Geba, K., Borrell, Y.J. & Garcia-Vazquez, E. (2014) DNA barcoding reveals a high level of mislabeling in Egyptian fish fillets. Food Control, 46, 441-445. https://doi.org/10.1016/j.foodcont.2014.06.016
  • Gao, Q.-F., Wang, Y., Dong, S., Sun, Z. & Wang, F. (2011) Absorption of different food sources by sea cucumber Apostichopus japonicus (Selenka) (Echinodermata: Holothuroidea): evidence from carbon stable isotope. Aquaculture, 319 (1-2), 272-276. https://doi.org/10.1016/j.aquaculture.2011.06.051
  • Gilliland, P.M. (1993) The skeletal morphology, systematics and evolutionary history of holothurians. Special Papers in Palaeontolgy, 47, 1-147.
  • Harmon, M. (2005) The Position of the Ophiuroidea within the Phylum Echinodermata. Available from: https://scholarcommons.usf.edu/etd/2916 (Accessed October 2021).
  • Hart, M.W. & Podolsky, R.D. (2005) Mitochondrial DNA phylogeny and rates of larval evolution in Macrophiothrix brittlestars. Molecular Phylogenetics and Evolution, 34 (2), 438-447. https://doi.org/10.1016/j.ympev.2004.09.011
  • Hasan, M.H. (2019) Destruction of sea cucumber populations due to overfishing at Abu Ghosoun area, Red Sea. The Journal of Basic and Applied Zoology, 80 (1), 1-10. https://doi.org/10.1186/s41936-019-0074-6
  • Hoareau, T.B. & Boissin, E. (2010) Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata. Molecular Ecology Resources, 10 (6), 960-967. https://doi.org/10.1111/j.1755-0998.2010.02848.x
  • Honey-Escandon, M., Laguarda-Figueras, A. & Solis-Marin, F.A. (2012) Molecular phylogeny of the subgenus Holothuria (Selenkothuria) Deichmann, 1958 (Holothuroidea: Aspidochirotida). Zoological Journal of the Linnean Society, 165 (1), 109-120. https://doi.org/10.1111/j.1096-3642.2011.00794.x
  • Honey-Escandon, M. & Solis-Marin, F. (2018) A revision of Holothuria (Halodeima) kefersteinii (Selenka, 1867) and the revival of Holothuria inornata Semper, 1868 from sea cucumbers collected in Mexico and Central America. Zootaxa, 4377 (2), 151-177. https://doi.org/10.11646/zootaxa.4377.2.1
  • Ismail, S.H. (2013) DNA Barcoding, Phylogenetic and Systematics of Holothuroidea (sea Cucumbers) in Malaysian Waters Based on 16s RRNA and Cytochrome Oxidase I (COI) Genes. Available from: http://eprints.usm.my/46241/1/Siti%20Has mah%20Binti%20Ismail24.pdf (accessed October 2021)
  • Kamarudin, K.R., Hashim, R. & Usup, G. (2010) Phylogeny of sea cucumber (Echinodermata: Holothuroidea) as inferred from 16S mitochondrial rRNA gene sequences. Sains Malaysiana, 39, 209-218.
  • Kamarudin, K.R., Rehan, M.M., Noor, H.M., Ramly, N.Z. & Rehan, A.M. (2016) 16S rRNA Barcoding technique for species identification of processed sea cucumbers from selected malaysian markets. Journal of Science and Mathematics Letters, 4, 10-23.
  • Kamarudin, K.R., Rehan, M.M. & Rehan, A.M. (2019) Species identification of processed sea cucumbers from Malaysian market based on concatenated gene sequences of mitochondrial rRNA genes. Maritime Technology and Research, 1 (2), 28-44. https://doi.org/10.33175/mtr.2019.146259
  • Kim, S.W., Kerr, A.M. & Paulay, G. (2013) Colour, confusion, and crossing: resolution of species problems in Bohadschia (Echinodermata: Holothuroidea). Zoological Journal of the Linnean Society, 168 (1), 81-97. https://doi.org/10.1111/zoj.12026
  • Lafay, B., Smith, A. & Christen, R. (1995) A combined morphological and molecular approach to the phylogeny of asteroids (Asteroidea: Echinodermata). Systematic Biology, 44 (2), 190-208. https://doi.org/10.2307/2413706
  • Lawrence, A.J., Ahmed, M., Hanafy, M., Gabr, H., Ibrahim, A. & Gab-Alla, A.A.F.A. (2005) Status of the sea cucumber fishery in the Red Sea-the Egyptian experience. FAO Fisheries Technical Paper, 79-90.
  • Letunic, I. & Bork, P. (2019) Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research, 47 (W1), W256-W259. https://doi.org/10.1093/nar/gkz239
  • Littlewood, D.T. (1994) Molecular phylogenetics of cupped oysters based on partial 28S rRNA gene sequences. Molecular Phylogenetics and Evolution, 3 (3), 221-229. https://doi.org/10.1006/mpev.1994.1024
  • Littlewood, D.T.J., Smith, A.B., Clough, K.A. & Emson, R.H. (1997) The interrelationships of the echinoderm classes: Morphological and molecular evidence. Biological Journal of the Linnaean Society, 61 (3), 409-438. https://doi.org/10.1111/j.1095-8312.1997.tb01799.x
  • Maggi, C. & Gonzalez-Wanguemert, M. (2015) Genetic differentiation among populations in the Western Mediterranean Sea: potential effects from its fishery and current connectivity. Mediterranean Marine Science, 16 (3), 489-501. https://doi.org/10.12681/mms.1020
  • Mahdy, A.A., Omar, H.A., Nasser, S.A.M., Abd El-Wakeil, K.F. & Obuid-Allah, A.H. (2019) Community structure of Echinoderms in littoral zone of the Red Sea Coast of Egypt. Egyptian Journal of Aquatic Biology and Fisheries, 22 (5), 483- 498. https://doi.org/10.21608/ejabf.2019.26814
  • Miller, A.K., Kerr, A.M., Paulay, G., Reich, M., Wilson, N.G., Carvajal, J.I. & Rouse, G.W. (2017) Molecular phylogeny of extant Holothuroidea (Echinodermata). Molecular Phylogenetics and Evolution, 111, 110-131. https://doi.org/10.1016/j.ympev.2017.02.014
  • Mortensen, T.H. (1943) A Monograph of the Echinoidea, Vol. 3, No. 2 Camarodonta. I. Orthopsidae, Glyphocyphidae, Temnopleuridae and Toxopneustidae-Atlas. CA Reitzel, Copenhagen, vii + 553 pp.
  • Moussa, R. & Wirawati, I. (2018) Observations on some biological characteristics of Holothuria polii and Holothuria sanctori from Mediterranean Egypt. International Journal of Fisheries and Aquatic Studies, 6 (3), 351-357.
  • O'Loughlin, P.M., Paulay, G., VandenSpiegel, D. & Samyn,Y. (2007) New Holothuria species from Australia (Echinodermata: Holothuroidea: Holothuriidae), with comments on the origin of deep and cool holothuriids. Memoirs of Museum Victoria, 64, 35-52. https://doi.org/10.24199/j.mmv.2007.64.5
  • Omran, N.E., Salem, H.K., Eissa, S.H., Kabbash, A.M., Kandeil, M.A. & Salem, M.A. (2020) Chemotaxonomic study of the most abundant Egyptian sea-cucumbers using ultra-performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (HRMS). Chemoecology, 30 (1), 35-48. https://doi.org/10.1007/s00049-019-00296-y
  • Palumbi, S., Martin, A., Romano, S., McMillan, W.O., Stice, L. & Grabowski, G. (1991) The simple fool's guide to PCR, Ver. 2.0. University of Hawaii, Honolulu, 47 pp.
  • Perseke, M., Bernhard, D., Fritzsch, G., Brummer, F., Stadler, P.F. & Schlegel, M. (2010) Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: insights in phylogenetic relationships of Echinodermata. Molecular Phylogenetics and Evolution, 56 (1), 201-211. https://doi.org/10.1016/j.ympev.2010.01.035
  • Purcell, S.W., Lovatelli, A., Vasconcellos, M. & Ye, Y. (2010) Managing sea cucumber fisheries with an ecosystem approach. FAO Fisheries and Aquaculture Technical Paper, 50. Available from: https://hdl.handle.net/10535/6237 (accessed October 2021)
  • Purcell, S.W., Mercier, A., Conand, C., Hamel, J.F., Toral-Granda, M.V., Lovatelli, A. & Uthicke, S. (2013) Sea cucumber fisheries: global analysis of stocks, management measures and drivers of overfishing. Fish and Fisheries, 14 (1), 34-59. https://doi.org/10.1111/j.1467-2979.2011.00443.x
  • Rambaut, A., Drummond, A.J., Xie, D., Baele, G. & Suchard, M.A. (2018) Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Systematic Biology, 67 (5), 901-904. https://doi.org/10.1093/sysbio/syy032
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Hohna, S., Larget, B, Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61 (3), 539-542. https://doi.org/10.1093/sysbio/sys029
  • Roskov, Y., Ower, G., Orrell, T., Nicolson, D., Bailly, N., Kirk, P.M., Bourgoin, T., DeWalt, R.E., Decock, W., Nieukerken, E.van., Zarucchi, J. & Penev, L. (2019) Species 2000 & ITIS Catalogue of Life, 2019 Annual Checklist. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-884X. Available from: www.catalogueoflife.org/annual-checklist/2019 (accessed 12 October 3021)
  • Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E. & Sanchez-Gracia, A. (2017) DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34 (12), 3299-3302. https://doi.org/10.1093/molbev/msx248
  • Safari, R., Qasemi, S.A., Rezvani Gilkalaee, S. & Qafari, H. (2020) Population structure of Holothuria leucospilota in the north of Persian Gulf and Oman Sea using DNA sequencing method. Aquaculture Sciences, 7 (2), 42-51.
  • Sicuro, B., Piccinno, M., Gai, F., Cesarina, A.M., Danieli, A., Dapra, F. & Mioletti, S. (2012) Food Quality and Safety of Mediterranean Sea Cucumbers Holothuria tubulosa and Holothuria polii in Southern Adriatic Sea. Asian Journal of Animal and Veterinary Advances, 7 (9), 851-859. https://doi.org/10.3923/ajava.2012.851.859
  • Soliman, T., Fernandez-Silva, I. & Reimer, J.D. (2016a) Genetic population structure and low genetic diversity in the over-exploited sea cucumber Holothuria edulis Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island. Conservation Genetics, 17 (4), 811-821. https://doi.org/10.1007/s10592-016-0823-8
  • Soliman, T., Takama, O., Fernandez-Silva, I. & Reimer, J.D. (2016a) Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan. PeerJ, 4, e2410. https://doi.org/10.7717/peerj.2410
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30 (12), 2725-2729. https://doi.org/10.1093/molbev/mst197
  • Thompson, J.D., Higgins, D.G. & Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22 (22), 4673-4680. https://doi.org/10.1046/j.1365-294X.2003.01954.x
  • Toral-Granda, V. (2008) Population status, fisheries and trade of sea cucumbers in Latin America and the Caribbean. Sea cucumbers. A global review of fisheries and trade. FAO Fisheries and Aquaculture Technical Paper, 516, 213-229.
  • Uthicke, S. & Benzie, J.A.H. (2003) Gene flow and population history in high dispersal marine invertebrates: mitochondrial DNA analysis of Holothuria nobilis (Echinodermata: Holothuroidea) populations from the Indo-Pacific. Molecular Ecology, 12 (10), 2635-2648. https://doi.org/10.1046/j.1365-294X.2003.01954.x
  • Vergara-Chen, C., Gonzalez-Wanguemert, M., Marcos, C. & Perez-Ruzafa, A. (2010) Genetic diversity and connectivity remain high in Holothuria polii (Delle Chiaje 1823) across a coastal lagoon-open sea environmental gradient. Genetica, 138 (8), 895-906. https://doi.org/10.1007/s10709-010-9472-x
  • Ward, R.D., Holmes, B.H. & O'Hara, T.D. (2008) DNA barcoding discriminates echinoderm species. Molecular Ecology Resources, 8, 1202-1211. https://doi.org/10.1111/j.1755-0998.2008.02332.x
  • Weber, A.A.T., Stohr, S. & Chenuil, A. (2019) Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata). Molecular Phylogenetics and Evolution, 131, 138-148. https://doi.org/10.1016/j.ympev.2018.11.014
  • Wen, J. & Zeng, L. (2014) Use of species-specific PCR for the identification of 10 sea cucumber species. Chinese Journal of Oceanology and Limnology, 32 (6), 1257-1263. https://doi.org/10.1007/s00343-015-4050-9
  • Yamana, Y., Hayashibara, T., Yamamoto, M. & Setiamarga, D.H. (2019) First observation of the "double-faced X-framed cup ossicle" extracted from a deep sea holothurian in Japan. Zoosymposia, 15 (1), 203-211. https://doi.org/10.11646/zoosymposia.15.1.21