Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models

• Published in: Journal of cellular biochemistry 2020-08, Vol.121 (8-9), p.3837-3853
• Main Authors: Tasneem, Fareeda, Shakoori, Farah R., Ilyas, Muhammad, Shahzad, Naveed, Potekhin, Alexey, Shakoori, Abdul R.
• Format: Article
• Language: English
• Subjects: 18S rDNA; Biomarkers; Ciliates; Comparative studies; Conserved sequence; Cytochrome; Cytochrome-c oxidase; Cytochromes; Deoxyribonucleic acid; DNA; DNA barcoding; Eukaryotes; Genetic diversity; Helices; Hsp70; Hsp70 protein; internal transcribed spacer regions; ITS1 and ITS2 secondary structures; mitochondrial cytochrome c oxidase subunit II; Nucleotides; Paramecium; Phylogenetics; Phylogeny; Polymerase chain reaction; Protein structure; Reaction products; Recombinant DNA; Secondary structure; Species; Species diversity; Taxonomy
• ISSN: 0730-2312; 1097-4644
• DOI: 10.1002/jcb.29546

Among ciliates, Paramecium has become a privileged model for the study of “species problem” particularly in the case of the “Paramecium aurelia complex” that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing‐alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1‐5.8S‐ITS2‐5′LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level. Secondary structures of the internal transcribed spacer 1 RNA transcript of (a) FT2.1, (b) FT8, (c) Paramecium caudatum, (d) P. multimicronucleatum, (e) P. polycaryum, and other ciliates, that is, (f) Tetrahymena thermopihla, (g) Stylonychia mytilus, and (h) Urocentrum turbo. The diagram illustrates the three helices: A, B, and C. Thick bars indicate highly conserved pairings. (a) Substitutions of FT2.1 strain as compared with P. tetraurelia species from GenBank are highlighted in red c