Abstract
The free-living amoebae of the genus Acanthamoeba are widely investigated for their diversity and evolution. Studies usually employ biomolecular methods targeting the 18S rRNA gene, assigning strains according to a well-established genotyping system. Strains from at least four genotypes contain introns in their rDNA. By retracing the evolutionary history of these introns within the amoebae, we found that the 18S rDNA of TUMSJ-341 strain (ATCC PRA-11), assigned to the genotype T5 (A. lenticulata), proved very unusual in our analyses, not corresponding to the characteristics of the group. The sequence contains a group I intron recovered only in A. lenticulata. At BLAST, however, the intron-less 18S rDNA of TUMSJ-341 does not match with T5 strains but shows some affinity with strains from genotype T4, suggesting a new genotype. Our accurate analysis of this sequence finally revealed a mixture of variable regions, showing that such discordant results are due to the insertion into the gene of a strain T5 of a DNA fragment containing hypervariable regions specific for a T4 strain. Data presented herein indicate that this sequence is probably a chimera.
This is a preview of subscription content, log in via an institution to check access.
References
Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71(12):8966–8969. https://doi.org/10.1128/AEM.71.12.8966-8969.2005
Booton GC, Kelly DJ, Chu YW, Seal DV, Houang E, Lam DS, Byers TJ, Fuerst PA (2002) 18S ribosomal DNA typing and tracking of Acanthamoeba species isolates from corneal scrape specimens, contact lenses, lens cases, and home water supplies of Acanthamoeba keratitis patients in Hong Kong. J Clin Microbiol 40(5):1621–1625. https://doi.org/10.1128/JCM.40.5.1621-1625.2002
Corsaro D, Venditti D (2010) Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida). Parasitol Res 107(1):233–238. https://doi.org/10.1007/s00436-010-1870-6
Corsaro D, Venditti D (2018a) An apparent Acanthamoeba genotype is the product of a chimeric 18S rDNA artefact. Parasitol Res 117(2):571–577. https://doi.org/10.1007/s00436-017-5690-9
Corsaro D, Venditti D (2018b) Nuclear group I introns with homing endonuclease genes in Acanthamoeba genotype T4. Eur J Protistol 66:26–35. https://doi.org/10.1016/j.ejop.2018.07.002
Corsaro D, Walochnik J, Köhsler M, Rott MB (2015) Acanthamoeba misidentification and multiple labels: redefining genotypes T16, T19 and T20, and proposal for Acanthamoeba micheli sp. nov. (genotype T19). Parasitol Res 114(7):2481–2490. https://doi.org/10.1007/s00436-015-4445-8
Corsaro D, Köhsler M, Montalbano Di Filippo M, Venditti D, Monno R, Di Cave D, Berrili F, Walochnik J (2017) Update on Acanthamoeba jacobsi genotype T15, including full-length 18S rDNA molecular phylogeny. Parasitol Res 116(4):1273–1284. https://doi.org/10.1007/s00436-017-5406-1
Fonseca VG, Nichols B, Lallias D, Quince C, Carvalho GR, Power DM, Creer S (2012) Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Res 40(9):e66. https://doi.org/10.1093/nar/gks002
Gast RJ, Ledee DR, Fuerst PA, Byers TJ (1996) Subgenus systematics of Acanthamoeba: four nuclear 18S rDNA sequence types. J Eukaryot Microbiol 43(6):498–504. https://doi.org/10.1111/j.1550-7408.1996.tb04510.x
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, The Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Res 21(3):494–504. https://doi.org/10.1101/gr.112730.110
Horn M, Fritsche TR, Linner T, Gautom RK, Harzenetter MD, Wagner M (2002) Obligate bacterial endosymbionts of Acanthamoeba spp. related to the β-Proteobacteria: proposal of ‘Candidatus Procabacter acanthamoebae’ gen. nov., sp. nov. Int J Syst Evol Microbiol 52(2):599–605. https://doi.org/10.1099/ijs.0.01970-0
Hugenholtzt P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53(1):289–293. https://doi.org/10.1099/ijs.0.02441-0
Khan NA (2009) Acanthamoeba—biology and pathogenesis. Caister Academic Press, Norfolk 290 pp
Mathers WD, Nelson SE, Lane JL, Wilson ME, Allen RC, Folberg R (2000) Confirmation of confocal microscopy diagnosis of Acanthamoeba keratitis using polymerase chain reaction analysis. Arch Ophthalmol 118(2):178–183. https://doi.org/10.1001/archopht.118.2.178
Page FC (1988) A new key to freshwater and soil Gymnamoebae. Freshwater Biological Association, Ambleside, pp 92–97
Risler A, Coupat-Goutaland B, Pélandakis M (2013) Genotyping and phylogenetic analysis of Acanthamoeba isolates associated with keratitis. Parasitol Res 112(11):3807–3816. https://doi.org/10.1007/s00436-013-3572-3
Schroeder JM, Booton GC, Hay J, Niszl IA, Seal DV, Markus MB, Fuerst PA, Byers TJ (2001) Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of Acanthamoebae from humans with keratitis and from sewage sludge. J Clin Microbiol 39(5):1903–1911. https://doi.org/10.1128/JCM.39.5.1903-1911.2001
Schroeder-Diedrich JM, Fuerst PA, Byers TJ (1998) Group-I introns with unusual sequences occur at three sites in nuclear 18S rRNA genes of Acanthamoeba lenticulata. Curr Genet 34(1):71–78. https://doi.org/10.1007/s002940050368
Stothard DR, Schroeder-Diedrich JM, Awwad MH, Gast RJ, Ledee DR, Rodriguez-Zaragoza S, Dean CL, Fuerst PA, Byers TJ (1998) The evolutionary history of the genus Acanthamoeba and the identification of eight new 18S rRNA gene sequence types. J Eukaryot Microbiol 45(1):45–54. https://doi.org/10.1111/j.1550-7408.1998.tb05068.x
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that there is no conflict of interest.
Additional information
Handling editor: Julia Walochnik
Rights and permissions
About this article
Cite this article
Corsaro, D., Venditti, D. Unusual 18S rDNA of Acanthamoeba containing intron turned out to be a T5/T4 chimera. Parasitol Res 118, 657–662 (2019). https://doi.org/10.1007/s00436-018-6136-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00436-018-6136-8