Exploring genome architecture, protein evolution and epigenetic processes in ciliates

Abstract

Ciliates are a diverse clade of unicellular eukaryotes that differ in size, morphology, and nuclear organization; they are characterized by both cilia and dimorphic nuclei. Three classes of ciliates extensively fragment their somatic macronuclear genome, a process that is associated with elevated rates of protein evolution. Although ciliates in the class Heterotrichea are not known to extensively fragment their somatic genome, they do show high levels of genome amplification. In this study, I examine how genome architecture affects patterns of molecular evolution within the class Heterotrichea. I use a combination of molecular and bioinformatic tools to determine copy number of paralogs and analyze patterns of protein evolution. The genome (PCR) data suggest that heterotrichs have few paralogs, and those that are present exhibit high levels of amino acid conservation. The transcriptome (high throughput sequence; HTS) data suggest that heterotrichs have many paralogs, which are variably conserved. Moreover, the qPCR data suggest Blepharisma americanum (Heterotrichea) has a high copy number of the SSU rDNA gene and a similar copy number among selected actin, α-tub and Ef1α paralogs. In contrast, the copy number varies significantly between genes of other ciliates that amplify their somatic genomes. Ciliates, with their unusual nuclei, can teach us about genome architecture and protein evolution