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DNA Barcoding for Diophrys quadrinucleata (Ciliophora: Euplotia) from South Korea

  • Chae, Kyu-Seok (Department of Biological Sciences and Bioengineering, Inha University) ;
  • Min, Gi-Sik (Department of Biological Sciences and Bioengineering, Inha University)
  • Received : 2022.05.10
  • Accepted : 2022.09.02
  • Published : 2022.10.31

Abstract

One marine ciliate, Diophrys quadrinucleata Zhang et al., 2020 was newly recorded from South Korea in this study. We provided morphological diagnosis and images of the Korean D. quadrinucleata population. We determined the small subunit ribosomal DNA (SSU rDNA) and cytochrome oxidase subunit I (CO1) sequence data of D. quadrinucleata, and then the sequences were compared with other Diophrys species. Intra-specific variation between the Korean and type (Chinese) populations was identical in the SSU rDNA, while the inter-specific variations between seven Diophrys species were 0.3-3.8% in the SSU rDNA and 12.6-18.2% in the CO1. In this study, we obtained 18S and CO1 data from species with identified morphology. As the importance of securing 18S and CO1 based on morphology increases in current studies, this study will contribute to ciliate studies.

Keywords

Acknowledgement

This study was supported by research funds from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202102203).

References

  1. Barth D, Krenek S, Fokin SI, Berendonk TU, 2006. Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome c oxidase I sequences. Journal of Eukaryotic Microbiology, 53:20-25. https://doi.org/10.1111/j.1550-7408.2005.00068.x
  2. Chantangsi C, Lynn DH, 2008. Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes. Molecular Phylogenetics and Evolution, 49:979-987. https://doi.org/10.1016/j.ympev.2008.09.017
  3. Dunthorn M, Foissner W, Katz LA, 2011. Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker. Protist, 162:85-99. https://doi.org/10.1016/j.protis.2010.06.003
  4. Foissner W, 2014. An update of 'basic light and scanning electronmicroscopic methods for taxonomic studies of ciliated protozoa'. International Journal of Systematic and Evolutionary Microbiology, 64:271-292. https://doi.org/10.1099/ijs.0.057893-0
  5. Gentekaki E, Lynn DH, 2009. High-level genetic diversity but no population structure inferred from nuclear and mitochondrial markers of the peritrichous ciliate Carchesium polypinum in the Grand River Basin (North America). Applied and Environmental Microbiology, 75:3187-3195. https://doi.org/10.1128/AEM.00178-09
  6. Hall T, 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41:95-98.
  7. Jung JH, Park MH, Kim SY, Choi JM, Min GS, Kim YO, 2017. Checklist of Korean ciliates(Protozoa: Ciliophora). Journal of Species Research, 6:241-257. https://doi.org/10.12651/JSR.2017.6.3.241
  8. Jung JH, Park KM, Min GS, 2012. Morphology, morphogenesis, and molecular phylogeny of a new brackish water ciliate, Pseudourostyla cristatoides n. sp., from Songjiho lagoon on the coast of East Sea, South Korea. Zootaxa, 3334:42-54. https://doi.org/10.11646/zootaxa.3334.1.3
  9. Jung SJ, Im EY, Struder-Kypke MC, Kitamura SI, Woo PTK, 2011. Small subunit ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 gene sequences of 21 strains of the parasitic scuticociliate Miamiensis avidus (Ciliophora, Scuticociliatia). Parasitology Research, 108:1153-1161. https://doi.org/10.1007/s00436-010-2157-7
  10. Kher CP, Doerder FP, Cooper J, Ikonomi P, Achilles-Day U, Kupper FC, Lynn DH, 2011. Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I(cox1) barcode. Protist, 162:2-13. https://doi.org/10.1016/j.protis.2010.03.004
  11. Kwon CB, Lee ES, Shin MK, 2008. Redescriptions of Diophrys appendiculata and D. scutum (Ciliophora: Spirotrichea: Uronychiidae) new to Korea. Korean Journal of Systematic Zoology, 24:191-197.
  12. Kwon CB, Shin MK, 2006. Redescription of previously unknown euplotine ciliates, Euplotes charon and Diophrys oligothrix (Ciliophora: Spirotrichea: Euplotida), from Korea. Korean Journal of Systematic Zoology, 22:29-35.
  13. Lynn DH, Struder-Kypke MC, 2006. Species of Tetrahymena identical by small subunit rRNA. gene sequences are discriminated by mitochondrial cytochrome c oxidase I gene sequences. Journal of Eukaryotic Microbiology, 53:385-387. https://doi.org/10.1111/j.1550-7408.2006.00116.x
  14. Lynn HD, 2008. The ciliated protozoa: characterization, classification and guide to the literature. Springer, New York, pp. 1-605.
  15. Medlin L, Elwood HJ, Stickel S, Sogin ML, 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene, 71:491-499. https://doi.org/10.1016/0378-1119(88)90066-2
  16. Park MH, Jung JH, Jo E, Park KM, Baek YS, Kim SJ, Min GS, 2018. Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora). Mitochondrial DNA Part A, DNA Mapping, Sequencing, and Analysis, 30:148-155. https://doi.org/10.1080/24701394.2018.1464563
  17. Song W, Li J, Liu W, Al-Rasheid KAS, Hu X, Lin X, 2014. Taxonomy and molecular phylogeny of four Strombidium species, including description of S. pseudostylifer sp. nov. (Ciliophora, Oligotrichia). Systematics and Biodiversity, 13:76-92. https://doi.org/10.1080/14772000.2014.970674
  18. Tamura K, Stecher G, Kumar S, 2021. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38:3022-3027. https://doi.org/10.1093/molbev/msab120
  19. Tarcz S, Potekhin A, Rautian M, Przybos E, 2012 Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea). Molecular Phylogenetics and Evolution, 63:500-509. https://doi.org/10.1016/j.ympev.2012.01.024
  20. Tarcz S, Przybos E, Surmacz M, 2013. An assessment of haplotype variation in ribosomal and mitochondrial DNA fragments suggests incomplete lineage sorting in some species of the Paramecium aurelia complex (Ciliophora, Protozoa). Molecular Phylogenetics and Evolution, 67:255-265. https://doi.org/10.1016/j.ympev.2013.01.016
  21. Tarcz S, Rautian M, Potekhin A, Sawka N, Beliavskaya A, Kiselev A, Nekrasova I, Przyboa E, 2014. Paramecium putrinum (Ciliophora, Protozoa): the first insight into the variation of two DNA fragments- Molecular support for the existence of cryptic species. Molecular Phylogenetics and Evolution, 73:140-145. https://doi.org/10.1016/j.ympev.2014.01.019
  22. Zhang C, Huang J, Ye T, Lu B, Chen X, 2020. The morphology and phylogeny of three Diophrys ciliates collected from the subtropical waters of China, including a new species (Ciliophora; Euplotia). Journal of Ocean University of China, 19:975-987. https://doi.org/10.1007/s11802-020-4536-8
  23. Zhao Y, Gentekaki E, Yi Z, Lin X, 2013. Genetic differentiation of the mitochondrial cytochrome oxidase c subunit I gene in genus Paramecium (Protista, Ciliophora). PLoS ONE, 8:e77044. https://doi.org/10.1371/journal.pone.0077044
  24. Zhao Y, Yi Z, Gentekaki E, Zhan A, Al-Farraj SA, Song W, 2016. Utility of combining morphological characters, nuclear and mitochondrial genes: an attempt to resolve the conflicts of species identification for ciliated protists. Molecular Phylogenetics and Evolution, 94:718-729. https://doi.org/10.1016/j.ympev.2015.10.017