High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous CiliateCarchesium polypinumin the Grand River Basin (North America)

Abstract

Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers-ITS1, ITS2, and the hypervariable regions of the large subunit rRNA-and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.Studies of intraspecific genetic variation in macroorganisms have provided insights into microevolutionary processes and speciation in these organisms. However, our understanding of the intraspecific genetic diversity of microbial eukaryotes and its temporal and spatial distribution is neither deep nor broad due to the limited number of studies that deal with these topics (2,5,7,31).Many of the studies assessing within-species genetic variation and its distribution have used random amplified polymorphic DNA (RAPD) fingerprinting. Typically, the amount of genetic variation is very low within a species (35,36,56), with some exceptions (20, 57). However, there are several problems arising from the use of RAPDs as the sole source of data, including reproducibility and scoring concerns (54).Sequences of the internal transcribed spacers (ITS), namely, ITS1 and ITS2, of the rRNA region have also been used to study the genetic diversity and population structure of protists (2, 6, 44). In several instances, the ITS sequences of populations of ciliates from across the globe have been nearly identical, indicating very low genetic variation (4, 13, 59, 62). On the other hand, the hypervariable regions of the large subunit (LSU) rRNA have revealed moderate genetic diversity in ciliates at the population level (15, 51).Mitochondrial DNA (mtDNA) has been employed only sparingly in population studies of protists, even though it is routinely used in similar studies of metazoans (3,7,8). Of the mitochondrial genes, the apocytochrome b gene (cob) and the cytochrome c oxidase I (cox-1) gene (cox-1) have been used for population-level analyses of ciliates. Estimation of intraspecific nucleotide diversity of the cob gene from three species of the prostome ciliate Coleps showed only minor differences (5). On the other hand, the cox-1 gene revealed genetic diversity that...

Comparative analysis of the mitochondrial cytochromecoxidase subunit I (COI) gene in ciliates (Alveolata, Ciliophora) and evaluation of its suitability as a biodiversity marker

“…During the last decade, with an increased number of molecular methods available and, hence, more molecular studies being performed, the number of taxa that possess these complexes is also bound to increase. A recent study on the peritrich ciliate species Carchesium polypinum has shown considerable genetic diversity among populations (Gentekaki & Lynn, 2009). Not knowing whether a cluster with large genetic distances (e.g.…”

“…The study by Gentekaki & Lynn (2009) showed high intraspecific divergence among populations of the peritrich species Carchesium polypinum, present in the COI gene, but not in nuclear genes. However, these three genera are representatives of only one class, the Oligohymenophorea, of the 11 classes within the Phylum Ciliophora (Lynn, 2008), and the genetic divergence, based on small subunit ribosomal RNA (SSU rRNA) gene sequences, is high within the phylum.…”

“…The COI gene is on average 2000-2200 nucleotides long. The characteristic feature of ciliate COI is a 108 amino acid insert in the first half of the gene, present in all species sequenced so far (Pritchard et al, 1986;Ziaie & Suyama, 1987;Pritchard et al, 1990b;Burger et al, 2000;Brunk et al, 2003;Barth et al, 2006;Lynn & Strüder-Kypke, 2006;Snoke et al, 2006;Chantangsi et al, 2007;Guggiari & Peck, 2008;Przyboś et al, 2008;Catania et al, 2009;Gentekaki & Lynn, 2009;Segade et al, 2009). This insert is located in the so-called barcoding region, used to discriminate species based on sequence divergence (Hebert et al, 2003a(Hebert et al, , 2003b.…”

Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa)

“…Until now two DNA regions have most frequently been used in P. aurelia studies: ribosomal (ITS1-5.8S-ITS2-5'LSU rDNA), and mitochondrial (a part of COI gene) regions . Moreover these regions have been proposed as a DNA barcoding tool for other ciliates (Strüder-Kypke and Lynn 2010; Stoeck et al 2014b), and have been used as a markers for population studies in particular ciliates (Gentekaki and Lynn 2009;Zufall et al 2012) as well as in several Paramecium species (Snoke et al 2006;Zhao et al 2013).…”

Morphometric study of a Brazilian strain of Carchesium polypinum (Ciliophora: Peritrichia) attached to Pomacea figulina (Mollusca: Gastropoda), with notes on a high infestation

“…Studies emphasizing genetic variation within-species are needed to determine whether C. polypinum collected from different sites around the world could be considered a single genetic unit. For example, GENTEKAKI & LYNN (2009) concluded that colonies of C. polypinum isolated from different locations in the Grand River basin in Southwestern Ontario, Canada, probably are not a single morphospecies as previously thought.…”