An assessment on the intrapopulational and intraindividual genetic diversity in LSU rDNA in the harmful algal blooms-forming dinoflagellate Margalefidinium (= Cochlodinium) fulvescens based on clonal cultures and bloom samples from Jiaozhou Bay, China

Harmful Algae - Tập 96 - Trang 101821 - 2020
Siheng Lin1,2, Zhangxi Hu1,3,4, Yunyan Deng1,3,4, Lixia Shang1,3,4, Christopher J. Gobler5, Ying Zhong Tang1,3,4
1CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
2University of Chinese Academy of Sciences, Beijing, 100049, China
3Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
4Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
5School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, USA

Tài liệu tham khảo

Bachvaroff, 2012, Molecular diversity of the syndinean genus Euduboscquella based on single-cell PCR analysis, Appl. Environ. Microbiol., 78, 334, 10.1128/AEM.06678-11 Baverstock, 1990, Ribosomal RNA nucleotide sequence: a comparison of newer methods used for its determination, and its use in phylogenetic analysis, Aust. Syst. Bot., 3, 101, 10.1071/SB9900101 Ben-Gharbia, 2016, Toxicity and growth assessments of three thermophilic benthic dinoflagellates (Ostreopsis cf. ovata, Prorocentrum lima and Coolia monotis) developing in the Southern Mediterranean Basin, Toxins, 8, 297, 10.3390/toxins8100297 Bolch, 2007, A review of the molecular evidence for ballast water introduction of the toxic dinoflagellates Gymnodinium catenatum and the Alexandrium "tamarensis complex" to Australasia, Harmful Algae, 6, 465, 10.1016/j.hal.2006.12.008 Clement, 2000, TCS: a computer program to estimate gene genealogies, Mol. Ecol., 9, 1657, 10.1046/j.1365-294x.2000.01020.x Daugbjerg, 2000, Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of three new genera of unarmoured dinoflagellates, Phycologia, 39, 302, 10.2216/i0031-8884-39-4-302.1 de Salas, 2003, Takayama Gen, Nov (Gymnodiniales, Dinophyceae), a new genus of unarmored Dinoflagellates with sigmoid apical grooves, including the description of two new species, J. Phycol., 39, 1233, 10.1111/j.0022-3646.2003.03-019.x Doblin, 2004, Transport of the harmful bloom alga Aureococcus anophagefferens by oceangoing ships and coastal boats, Appl. Environ. Microbiol, 70, 6495, 10.1128/AEM.70.11.6495-6500.2004 Dover, 1982, Molecular drive: a cohesive mode of species evolution, Nature, 299, 111, 10.1038/299111a0 Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381 Excoffier, 2010, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 10, 564, 10.1111/j.1755-0998.2010.02847.x Galluzzi, 2010, Analysis of rRNA gene content in the Mediterranean dinoflagellate Alexandrium catenella and Alexandrium taylori: implications for the quantitative real-time PCR-based monitoring methods, J. Appl. Phycol., 22, 1, 10.1007/s10811-009-9411-3 Gárate-Lizárraga, 2014, Ocurrencia de Cochlodinium fulvescens (gymnodiniales: dinophyceae) en el suroeste del Golfo de California, Rev. Biol. Mar. Oceanogr., 49, 123, 10.4067/S0718-19572014000100013 Gárate-Lizárraga, 2008, First record of Cochlodinium fulvescens in Mexican Pacific, Harmful Algae News, 37, 5 Godhe, 2008, Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR, Appl. Environ. Microbiol., 74, 7174, 10.1128/AEM.01298-08 Gómez, 2017, Molecular characterization and morphology of Cochlodinium strangulatum, the type species of Cochlodinium, and Margalefidinium gen. nov. for C. polykrikoides and allied species (Gymnodiniales, Dinophyceae), Harmful Algae, 63, 32, 10.1016/j.hal.2017.01.008 Gribble, 2007, High intraindividual, intraspecific, and interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae), Phycologia, 46, 315, 10.2216/06-68.1 Guillard, 1975, Culture of phytoplankton for feeding marine invertebrates, 29 Hallegraeff, 2012, Global toxicology, ecophysiology and population relationships of the chainforming PST dinoflagellate Gymnodinium catenatum, Harmful Algae, 14, 130, 10.1016/j.hal.2011.10.018 Hassouna, 1984, The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA In higher eukaryotes, Nucleic Acids Res., 12, 3563, 10.1093/nar/12.8.3563 Hillis, 1989, 355 Hillis, 1991, Ribosomal DNA: molecular evolution and phylogenetic inference, Q. Rev. Biol., 66, 411, 10.1086/417338 Hou, 2009, Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes, PLoS One, 4, e6978, 10.1371/journal.pone.0006978 Howard, 2012, Quantitative real-time PCR for Cochlodinium fulvescens (Dinophyceae), a potentially harmful dinoflagellate from California coastal waters, J. Phycol., 48, 384, 10.1111/j.1529-8817.2012.01120.x Hu, 2018, The morphological and phylogenetic characterization for the dinoflagellate Margalefidinium fulvescens (= Cochlodinium fulvescens) isolated from the Jiaozhou Bay, China, Acta Oceanol. Sin., 37, 11, 10.1007/s13131-018-1295-0 Iwataki, 2007, Cochlodinium fulvescens sp. nov. (Gymnodiniales, Dinophyceae), a new chain-forming unarmored dinoflagellate from Asian coasts, Phycol. Res., 55, 231, 10.1111/j.1440-1835.2007.00466.x Iwataki, 2008, Phylogenetic relationships in the harmful dinoflagellate Cochlodinium polykrikoides (Gymnodiniales, Dinophyceae) inferred from LSU rDNA sequences, Harmful Algae, 7, 271, 10.1016/j.hal.2007.12.003 Karafas, 2017, An evaluation of the genus Amphidinium (Dinophyceae) combining evidence from morphology, phylogenetics, and toxin production, with the introduction of six novel species, Harmful Algae, 68, 128, 10.1016/j.hal.2017.08.001 Iwataki, 2015, 551 Ki, 2006, A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain, Biosens. Bioelectron., 21, 1812, 10.1016/j.bios.2005.09.006 Kudela, 2012, Harmful dinoflagellate blooms caused by Cochlodinium sp.: global expansion and ecological strategies facilitating bloom formation, Harmful Algae, 14, 71, 10.1016/j.hal.2011.10.015 Kumar, 2016, MEGA7: molecular Biology and Evolutionics analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 33, 1870, 10.1093/molbev/msw054 Leigh, 2015, POPART: full‐feature software for haplotype network construction, Methods Ecol. Evol., 6, 1110, 10.1111/2041-210X.12410 Lenaers, 1989, Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA, J. Mol. Evol., 29, 40, 10.1007/BF02106180 Lin, 2011, Genomic understanding of dinoflagellates, Res. Microbiol., 162, 551, 10.1016/j.resmic.2011.04.006 Logares, 2009, Genetic diversity patterns in five protist species occurring in lakes, Protist, 160, 301, 10.1016/j.protis.2008.10.004 Luo, 2017, Cryptic diversity within the harmful dinoflagellate Akashiwo sanguinea in coastal Chinese waters is related to differentiated ecological niches, Harmful Algae, 66, 88, 10.1016/j.hal.2017.05.008 Lyu, 2017, LSU rDNA based RFLP assays for the routine identification of Gambierdiscus species, Harmful Algae, 66, 20, 10.1016/j.hal.2017.04.009 Markmann, 2005, Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences, Philos. Trans. R. Soc. Lond. B: Biol. Sci., 360, 1917, 10.1098/rstb.2005.1723 Mertens, 2015, Taxonomic re-examination of the toxic armored dinoflagellate Pyrodinium bahamense Plate 1906: Can morphology or LSU sequencing separate P. bahamense var. compressum from var. bahamense?, Harmful Algae, 41, 1, 10.1016/j.hal.2014.09.010 Miranda, 2012, Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex, Harmful Algae, 16, 35, 10.1016/j.hal.2012.01.002 Munir, 2012, First report of the athecate, chain forming dinoflagellate Cochlodinium fulvescens (Gymnodiniales) from Pakistan, Pak. J. Bot., 44, 2129 Murray, 2005, Improving the analysis of dinoflagellate phylogeny based on rDNA, Protist, 156, 269, 10.1016/j.protis.2005.05.003 Nei, 1987 Nishimura, 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 Price, 2012, FastTree 2 – approximately maximum-likelihood trees for large alignments, PLoS One, 5, e9490 Prokopowich, 2003, The correlation between rDNA copy number and genome size in eukaryotes, Genome, 46, 48, 10.1139/g02-103 Rambaut, A., 2009. FigTree v1.3.1: Tree Figure Drawing Tool. Edinburgh, UK. Reñé, 2015, Diversity and phylogeny of Gymnodiniales (Dinophyceae) from the NW Mediterranean Sea revealed by a morphological and molecular approach, Protist, 166, 234, 10.1016/j.protis.2015.03.001 Reñé, 2013, Phylogenetic relationships of Cochlodinium polykrikoides Margalef (Gymnodiniales, Dinophyceae) from the Mediterranean Sea and the implications of its global biogeography, Harmful Algae, 25, 39, 10.1016/j.hal.2013.02.004 Rengefors, 2017, Genetic diversity and evolution in eukaryotic phytoplankton: revelations from population genetic studies, J. Plankton Res., 39, 165 Rousset, 1997, Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance, Genetics, 145, 1219, 10.1093/genetics/145.4.1219 Rozas, 2003, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, 19, 2496, 10.1093/bioinformatics/btg359 Scholin, 1994, Identification of group- and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae). II. Sequence analysis of a fragment of the LSU rRNA gene, J. Phycol., 30, 999, 10.1111/j.0022-3646.1994.00999.x Shang, 2019, Metagenomic sequencing identifies highly diverse assemblages of dinoflagellate cysts in sediments from ships’ ballast tanks, Microorganisms, 7, 250, 10.3390/microorganisms7080250 Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75 Sonnenberg, 2007, An evaluation of LSU rDNA D1–D2 sequences for their use in species identification, Front. Zool., 4, 6, 10.1186/1742-9994-4-6 Tanabe, 2016, Comparative study of the validity of three regions of the 18S-rRNA gene for massively parallel sequencing-based monitoring of the planktonic eukaryote community, Mol. Ecol. Resour., 16, 402, 10.1111/1755-0998.12459 Tang, 2019, 3,000km and 1,500-year presence of Aureococcus anophagefferens reveals -indigenous origin of brown tides in China, Mol. Ecol, 28, 4065, 10.1111/mec.15196 Tautz, 2002, DNA points the way ahead in taxonomy, Nature, 418, 479, 10.1038/418479a Thangaraj, 2017, Molecular cloning reveals co-occurring species behind red tide blooms of the harmful dinoflagellate Cochlodinium polykrikoides, Biochem. Syst. Ecol., 70, 29, 10.1016/j.bse.2016.10.021 Varela, 2012, Intraregional variation among Alexandrium catenella (Dinophyceae) strains from southern Chile: morphological, toxicological and genetic diversity, Harmful Algae, 15, 8, 10.1016/j.hal.2011.10.029 Wang, 2020, Toxicity comparison among four strains of Margalefidinium polykrikoides from China, Malaysia, and USA (belonging to two ribotypes) and possible implications, J. Exp. Mar. Biol. Ecol., 524, 10.1016/j.jembe.2019.151293 Wang, 2019, Cryptic speciation in Protoceratium reticulatum (Dinophyceae): Evidence from morphological, molecular and ecophysiological data, Harmful Algae, 88, 10.1016/j.hal.2019.05.003 Weider, 2005, The functional significance of ribosomal (r) DNA variation: impacts on the evolutionary ecology of organisms, Annu. Rev. Ecol., Evol. Syst., 36, 219, 10.1146/annurev.ecolsys.36.102003.152620 Whyte, 2001, First record of blooms of Cochlodinium sp.(Gymnodiniales, Dinophyceae) causing mortality to aquacultured salmon on the west coast of Canada, Phycologia, 40, 298, 10.2216/i0031-8884-40-3-298.1 Wright, 1984 Wylezich, 2010, An evaluation of the use of the LSU rRNA D1–D5 domain for DNA-based taxonomy of eukaryotic protists, Protist, 161, 342, 10.1016/j.protis.2010.01.003 Yeung, 1996, Sequence data for two large-subunit rRNA genes from an Asian strain of Alexandrium catenella, Appl. Environ. Microbiol., 62, 4199, 10.1128/AEM.62.11.4199-4201.1996 Zhai, 2019, Morphological and ultrastructural comparison and phylogenetic analyses for the East asian and American/Malaysian ribotypes of Margalefidinium polykrikoides, Oceanol. Limnol. Sin., 50, 1252