Molecular characterization of toxic benthic dinoflagellate, Prorocentrum lima in west Indonesian waters using LSU 28S rDNA gene
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Abstract
Abstract. Widiarti R, Zamani NP, Bengen DG, Madduppa H. 2022. Molecular characterization of toxic benthic dinoflagellate, Prorocentrum lima in west Indonesian waters using LSU 28S rDNA gene. Biodiversitas 23: 3257-3263. Prorocentrum lima is one of the toxic benthic dinoflagellates known to cause Diarrhetic Shellfish Poisoning (DSP), which is also associated with ciguatoxin-producing species, Gambierdiscus toxicus that causes Ciguatera Fish Poisoning (CFP). P. lima has a wide range of morphological variability and genetic diversity, but such research has never been reported from Indonesian waters yet. This study aimed to determine the molecular characteristics of P. limain west Indonesian waters, namely Bintan Island, Belitung Island, Seribu Islands, and Karimunjawa Islands. Molecular characterization was conducted by amplification on large subunit (LSU)28S rDNA gene. Extraction was conducted using freeze-thaw which was continued with single cell PCR method. Genetic distance values and phylogenetic analysis were analyzed using MEGA software. Based on molecular analysis, P. lima from this research was divided into two subclades, namely subclade A from Seribu Islands and Belitung Island, and subclade B from Karimunjawa Islands and Bintan Island. P. lima from Bintan Island showed a closer relationship with the reference sequence from the Genbank. Observation of molecular characters of P. lima showed that the genetic diversity of P. lima depended on the variation of the island’s morphogenesis type.These findings could support a further study on the distribution of P. lima in Indonesian waters, related to the genetic variation and toxin production, since Indonesia consists of many small islands.
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References
Anzani L, Madduppa H, Nurjaya IW, Dias PJ. 2019. Short Communication: Molecular identification of White Sea Squirt Didemnum sp. (Tunicata, Ascidiacea) colonies growing over corals in Raja Ampat Islands, Indonesia. Biodiversitas 20(3): 636-642. doi: 10.13057/biodiv/d200304
Bolch C. 2001. PCR protocols for genetic identification of dinoflagellates directly from single cysts and plankton cells. Phycologia 40(2): 162-167.
Burkholder JM. 1998. Implications of harmful microalgae and heterotrophic dinoflagellates in management of sustainable marine fisheries. Ecological Applications 8(1): S37-S62.
Chomérat N, Bilien G, Zentz F. 2018. A taxonomical study of benthic Prorocentrum species (Prorocentrales, Dinophyceae) from Anse Dufour (Martinique Island, eastern Caribbean). Mar. Biodivers 49: 1299-1319. doi:10.1007/s12526-018-0913-6
Edvardsen B, Tabrizi KS, Jakobsen KS, Medlin LK, Dahl E, Brubak S, Paasche E. 2003. Genetic Variability and Molecular Phylogeny of Dinophysis Species (Dinophyceae) from Norwegian Waters Inferred from Single Cell Analyses of rDNA. J. Phycol 39: 395-408.
Fassler J, Cooper P. 2011. BLAST Glossary. BLAST® Help - NCBI Bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK62051
Grzebyk D, Sako Y, Berland B. 1998. Phylogenetic analysis of nine species of Prorocentrum (Dinophyceae) inferred from 18S Ribosomal DNA sequences, morphological comparisons, and description of Prorocentrum panamensis, sp. Nov. 1055. J. Phycol 34: 1055-1068.
Hoppenrath M, Chomérat N, Horiguchi T, Schweikert M, Nagahama Y, Murray S. 2013. Taxonomy and phylogeny of the benthic Prorocentrum species (Dinophyceae) - A proposal and review. Harmful Algae 27: 1-28. doi:10.1016/j.hal.2013.03.006
Hoppenrath M, Murray SA, Chomérat N, Horiguchi T. 2014. Marine Benthic Dinoflagellates: Unveiling Their Worldwide Biodiversity. Senckenberg-Reihe, Stuttgart.
Laza-Martinez A, Orive E, Miguel I. 2011. Morphological and genetic characterization of benthic dinoflagellates of the genera Coolia, Ostreopsis and Prorocentrum from the south-eastern Bay of Biscay. Eur. J. Phycol 46(1): 45-65.
Leaw CP, Lim PT, Ahmad A, Usup G. 2001. Genetic Diversity of Ostreopsis ovata (Dinophyceae) from Malaysia. Mar. Biotechnol 3: 246-255.
Lehane L, Lewis RJ. 2000. Ciguatera: recent advances but the risk remains. Int. J. Food. Microbiol 61: 91-125. doi:10.1016/S0168-1605(00)00382-2
Lenaers G, Maroteaux L, Michot B, Herzog M. 1989. Dinoflagellates in Evolution. A Molecular Phylogenetic Analysis of Large Subunit Ribosomal RNA. J Mol Evol 29: 40-51.
Luo Z, Zhang H, Krock B, Lu S, Yang W, Gu H. 2017. Morphology, molecular phylogeny and okadaic acid production of epibenthic Prorocentrum (Dinophyceae) species from the northern South China Sea. Algal Research 22: 14-30.
Marín I, Aguilera A, Reguera B, Abad JS. 2001. Preparation of DNA suitable for PCR amplification from fresh or fixed single dinoflagellate cells. BioTechniques 30: 88-93.
Menlove KJ, Clement M, Crandall KA. 2009. Similarity searching using BLAST. Methods in Molecular Biology: 1-22. doi: 10.1007/978-1-59745-251-9_1
Mordret S, Piredda R, Vaulot D, Montresor M, Kooistra WHCF, Sarno D. 2018. Dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol Ecol Resour 18: 974-987. doi: 10.1111/1755-0998.12781
Nagahama Y, Murray S, Tomaru A, Fukuyo Y. 2011. Species boundaries in the toxic dinoflagellate Prorocentrum lima (Dinophyceae, Prorocentrales), based on morphological and phylogenetic characters. J. Phycol 47(1): 178–189.
Nascimento SM, Mendes MCQ, Menezes M, Rodríguez F, Alves-de-Souza C, Branco S, Riobó P, Franco J, Nunes JMC, Huk M, Morris S, Fraga S. 2017. Morphology and phylogeny of Prorocentrum caipirignum sp. nov. (Dinophyceae), a new tropical toxic benthic dinoflagellate. Harmful Algae 70: 73–89.
Nishimura T, Uchida H, Noguchi R, Oikawa H, Suzuki T, Funaki H, Ihara C, Hagino K, Arimitsu S, Tanii Y, Abe S, Hashimoto K, Mimura K, Tanaka K, Yanagida I, Adachi M. 2019. Abundance of the benthic dinoflagellate Prorocentrum and the diversity, distribution, and diarrhetic shellfish toxin production of Prorocentrum lima complex and P. caipirignum in Japan. Harmful Algae 96: 1-17. doi.org/10.1016/j.hal.2019.101687
Newell PD, Fricker AD, Roco CA, Chandrangsu P, Merkel SM. 2013. A small-group activity introducing the use and interpretation of BLAST. J Microbiol Biol Educ 14(2): 238-243. doi: 10.1128/jmbe.v14i2.637
Scholin CA, Herzog M, Sogin M, Anderson DM. 1994. Identification of group- and strain-spesific genetic markers for globally distributed Alexandrium (Dinophyceae). II. Sequence analysis of a fragment of the LSU rRNA gene. J. Phycol 30: 999-1011.
Sebastian CR, O’ Ryan C. 2001. Single-cell sequencing of dinoflagellate (Dinophyceae) nuclear ribosomal genes. Molecular Ecology Notes 1: 329-331.
Seu Ki J, Soo Han M. 2008. Implications of complete nuclear large subunit ribosomal RNA molecules from the harmful unarmored dinoflagellate Cochlodinium polykrikoides (Dinophyceae) and relatives. Biochemical Systematics and Ecology 36: 573-583.
Steidinger K, Baden D. 1984. Toxic marine dinoflagellates. Di dalam: Spector D, editor. Dinoflagellates. Academic Press, New York.
Takano Y, Horiguchi T. 2005. Acquiring scanning electron microscopical, light microscopical and multiple gene sequence data from a single dinoflagellate cell. J. Phycol 42: 251-256.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2011. Mega 5: Molecular evolution genetics analysis version 6.0. Mol.Bio.Evo 30: 2725-2729.
Tawong W, Nishimura T, Sakanari H, Sato S, Yamaguchi H, Adachi M. 2015. Characterization of Gambierdiscus and Coolia (Dinophyceae) isolates from Thailand based on morphology and phylogeny. Phycol. Res 63: 125-133.
Thoha H. 2008. Identification of some strain of Dinoflagellate based on morphology and molecular analysis. Sains Makara 12(2): 69-74.
Thoha H, Muawanah, Intan MDB, Rachman A, Sianturi OR, Sidabutar T, Iwataki M, Takahashi K, Avarre JC, Masseret E. 2019. Resting cyst distribution and molecular identification of the harmful Dinoflagellate Margalefidinium polykrikoides (Gymnodiniales, Dinophyceae) in Lampung Bay, Sumatra, Indonesia. Frontiers in Microbiology 10: 306. doi: 10.3389/fmicb.2019.00306
Widiarti R. 2002. Dinoflagellata epibentik pada makroalga di rataan terumbu Pulau Penjaliran Barat, Teluk Jakarta. Sains Indonesia 7: 1-9.
Zhang H, Li Y, Cen J, Wang H, Cui L, Dong Y, Lu S. 2015. Morphotypes of Prorocentrum lima (Dinophyceae) from Hainan Island, South China Sea: Morphological and molecular characterization. Phycologia 54: 503-516. doi:10.2216/15-8.1
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