Document Type
Article
Publication Date
4-29-2016
Publication Title
Genome Biology and Evolution
Abstract
The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata , we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata , we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features.
Keywords
nuclear architecture, genome evolution, codon bias, in situ hybridization, Protist
Volume
8
Issue
6
First Page
1634
Last Page
1642
DOI
https://doi.org/10.1093/gbe/evw099
ISSN
1759-6653
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License
Rights
This article was originally published in Genome Biology and Evolution 2016; 8 (6): 1634-1642. doi: 10.1093/gbe/evw099.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/ ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Recommended Citation
Xyrus X. Maurer-Alcalá, Laura A. Katz; Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata. Genome Biol Evol 2016; 8 (6): 1634-1642. doi: 10.1093/gbe/evw099
Comments
Archived as published.