Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata

Abstract

While molecular analyses have provided insight into the phylogeny of ciliates, the few studies assessing intraspecific variation have largely relied on just a single locus (e.g. nuclear small subunit rDNA (nSSU-rDNA) or mitochondrial cytochrome oxidase I). In this study, we characterize the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA (mtSSU-rDNA) of five isolates of the ciliate morphospecies Chilodonella uncinata. Although these isolates have nearly identical nSSU-rDNA sequences, they differ by up to 8.0% in mtSSU-rDNA. Comparative analyses of all loci, including β-tubulin paralogs, indicate a lack of recombination between strains, demonstrating that the morphospecies C. uncinata consists of multiple cryptic species. Further, there is considerable variation in substitution rates among loci as some protein-coding domains are nearly identical between isolates while others differ by up to 13.2% at the amino acid level. Combining insights on macronuclear variation among isolates, the focus of this study, with published data from the micronucleus of two of these isolates indicates that C. uncinata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome.

Nanochromosome Copy Number Does not Correlate with RNA Levels Though Patterns are Conserved between Strains of the Ciliate Morphospecies Chilodonella uncinata

“…The two strains of C. uncinata (POL=ATCC® PRA-256, USA-SC2) used in this study were described previously (Katz et al 2011; Robinson and Katz 2007) and culturing conditions are as reported in these publications.…”

Analyses of chromosome copy number and expression level of four genes in the ciliate Chilodonella uncinata reveal a complex pattern that suggests epigenetic regulation

“…Five sequences from β-tubulin show variability in their degree of conservation. Two sequences, shared P1 (SP1) and shared P2 (SP2) are highly conserved (identical amino acid sequences and < 2 % difference at the nucleotide level) but three macronuclear chromosome P1, P2, and P3 are more divergent with up to 13.5 % nucleotide differences (Robinson and Katz, 2007; Katz et al, 2011). Recent analyses of the micronuclear loci from the β-tubulin gene family reveal that an alternative processing of scrambled genes generates some of the diversity in the macronuclear sequences of this family (Katz and Kovner, 2010).…”

“…We characterize these sequences from three cryptic species of the morphospecies C. uncinata , one isolated from Poland and two from different places in the United States (USA-ATCC and USA-SC2) as described in Katz et al (2011). We focus on the five β-tubulin chromosomes to assess the relationship between macronuclear copy number and expression patterns of gene family members.…”

Low-level genetic diversity of opalinid morphotypes from the digestive tract of Hoplobatrachus rugulosus (Batrachia, Amphibia) in Thailand

“…Typically, SSU rDNA is not used for lower than species level analyses. Rather, other less conserved markers are preferred, including the internal transcribed spacers (ITS), large subunit rDNA (LSUrDNA) and cytochrome c oxidase subunit 1 (cox1) (Gentekaki and Lynn 2010;Katz et al 2011;Saez et al 2003). Nonetheless, SSU rDNA has sometimes revealed substantial differences among seemingly identical isolates (Finlay et al 2006;Evans et al 2008).…”