TY - JOUR

T1 - Genetic diversity of Paramecium species on the basis of multiple loci describes the analysis and ITS secondary structure models

AU - Tasneem, Fareeda

AU - Shakoori, Farah R.

AU - Ilyas, Muhammad

AU - Shahzad, Naveed

AU - Potekhin, Alexey

AU - Shakoori, Abdul R.

PY - 2020/8/1

Y1 - 2020/8/1

N2 - 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.

AB - 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.

KW - 18S rDNA

KW - ciliates

KW - DNA barcoding

KW - Hsp70

KW - internal transcribed spacer regions

KW - ITS1 and ITS2 secondary structures

KW - mitochondrial cytochrome c oxidase subunit II

KW - EXISTENCE

KW - STRAINS

KW - PHYLOGENY

KW - SEQUENCES

KW - MOLECULAR EVOLUTION

KW - CILIOPHORA

KW - OLIGOHYMENOPHOREA

KW - CILIATES PROTISTA

KW - 18S RIBOSOMAL-RNA

KW - GENUS PARAMECIUM

UR - http://www.scopus.com/inward/record.url?scp=85074904253&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/genetic-diversity-paramecium-species-basis-multiple-loci-describes-analysis-secondary-structure-mode

U2 - 10.1002/jcb.29546

DO - 10.1002/jcb.29546

M3 - Article

AN - SCOPUS:85074904253

VL - 121

SP - 3837

EP - 3853

JO - Journal of Cellular Biochemistry

JF - Journal of Cellular Biochemistry

SN - 0730-2312

IS - 8-9

ER -