GENOME STRUCTURE DRIVES PATTERNS OF GENE FAMILY EVOLUTION IN CILIATES, A CASE STUDY USINGCHILODONELLA UNCINATA(PROTISTA, CILIOPHORA, PHYLLOPHARYNGEA)

Abstract

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that: 1) alternative processing is extensive among gene families; and 2) such gene families are likely to be C. uncinata-specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family -- a protein kinase domain containing protein (PKc) -- from two C. uncinata strains. Analysis of the PKc sequences reveals: 1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and 2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes.

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

“…Alternatively, the low expression of chromosomes may be related to their origins as the genes with the lowest expressions here, Pkc and Hap , are generated by alternative processing during macronuclear development (i.e. are generated using a combination of unique and shared micronuclear regions, Gao et al 2014). Two of the three rarely expressed β-tubulin members (Bellec and Katz 2012) are also generated from alternatively processing of micronuclear loci (Katz and Kovner 2010), suggesting that alternatively processed gene family members may be expressed at low levels during vegetative growth of C. uncinata .…”

Taxonomic studies on seven species of Dysteria (Ciliophora, Cyrtophoria), including a description of Dysteria paraprocera sp. n.

“…Genomic DNA was extracted using a DNeasy Tissue kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. TaKaRa ExTaq polymerase (TaKaRa Biomedicals, Japan) was used to amplify the SSU rRNA gene by universal primers (Medlin et al 1988) with PCR conditions following Gao et al (2014). Cloning and sequencing were performed as described by Gao et al (2014).…”

Hidden genetic variation in the germline genome of Tetrahymena thermophila

“…The dual nature of ciliate genomes has long been known; however, the evolutionary effects of this unusual genome architecture have yet to be fully understood. Previous work has demonstrated the effects of ciliate genome architecture on the rates of protein evolution (Zufall et al ., ), gene family evolution (Gao et al ., ) and mutation rate (Sung et al ., , H. Long, personal communication). Here, we found that Tetrahymena genome architecture allows for the maintenance of genetic variation for fitness in the micronuclear genome despite the low variation present in the macronuclear genome.…”