PgmNr C7001: Evolution of gene families in ciliates.

Authors:
O. A. Pilling 1 ; X. X. Maurer-Alcalá 1,2 ; L. A. Katz 1,2


Institutes
1) Smith College, Northampton, MA; 2) University of Massachusetts Amherst, Amherst, MA.


Abstract:

We use ciliates as a model to gain insight into how genome structure affects patterns of DNA sequence evolution. Previous research has demonstrated that ciliates, a clade of eukaryotes marked by dimorphic nuclei and cilia in at least one stage of their life cycle, have rapid rates of protein evolution associated with highly processed somatic genomes (Katz et al. 2003; Zufall et al. 2006). We are building on this work by investigating the protein evolution of three species of ciliates in the class Heterotrichea, which has previously been understudied.  Our focus is on characterizing patterns of divergenes among paralogs (i.e. genes that differ due to an ancient duplication events). For this project, we focus on the ciliates Blepharisma americanum, Stentor sp. and Spirostomum ambiguum, and six genes (Actin, α-tubulin, β-tubulin, Ef1-α, H3 and H4).

We chose to study B. americanum because preliminary data suggest they may have elevated rates of protein evolution (Zufall et al. 2006). Unlike the classes Spirotrichea, Armophorea and Phyllopharyngea where rates of protein evolution are associated with extensively processed somatic genomes (e.g. ‘gene-sized’ chromosomes), members of the Heterotrichea are not known to extensively modify their macronuclear genomes. We are using PCR based approach to analyze protein evolution and are interpreting the resulting data in a molecular evolution framework.

This project has included both wet work and bioinformatics. While the majority of the wet work is completed, we are now beginning to analyze the data by calculating the dN/dS ratio and performing pairwise comparisons. Through this approach, we can start to better understand the impact genome architecture has on molecular evolution.

Literature Cited:

Katz LA, Bornstein JG, Lasek-Nesselquist E, Muse SV. 2004. Dramatic diversity of ciliate Histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes. Mol Biol Evol. 21(3): 555-562.

Zufall RA, McGrath CL, Muse SV, Katz LA. 2006. Genome architecture drives protein evolution in ciliates. Mol Biol Evol. 23(9): 1681-1687.