Genome diversity in microbial eukaryotes

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Abstract

The genomic peculiarities among microbial eukaryotes challenge the conventional wisdom of genome evolution. Currently, many studies and textbooks explore principles of genome evolution from a limited number of eukaryotic lineages, focusing often on only a few representative species of plants, animals and fungi. Increasing emphasis on studies of genomes in microbial eukaryotes has and will continue to uncover features that are either not present in the representative species (e.g. hypervariable karyotypes or highly fragmented mitochondrial genomes) or are exaggerated in microbial groups (e.g. chromosomal processing between germline and somatic nuclei). Data for microbial eukaryotes have emerged from recent genome sequencing projects, enabling comparisons of the genomes from diverse lineages across the eukaryotic phylogenetic tree. Some of these features, including amplified rDNAs, subtelomeric rDNAs and reduced genomes, appear to have evolved multiple times within eukaryotes, whereas other features, such as absolute strand polarity, are found only within single lineages.

Section snippets

The diversity of microbial eukaryotes

Interpreting the evolution of eukaryotic genomes requires knowledge of the evolutionary relationships among eukaryotes, particularly among the microbial lineages. Microbial eukaryotes, or protists, are defined loosely as eukaryotic organisms that are not plants, animals or fungi. Reconstructing eukaryotic phylogeny has proven difficult, in part because there are few morphological characters that can be used to resolve deep nodes [1]. Similarly, there is considerable discordance among

Genome size

Even with the relatively limited data available from the genomes of microbial eukaryotes, it is evident that genome size varied tremendously during the evolution of the diverse lineages (Table 1). Extensive reviews of genome size can be found elsewhere (e.g. 14, 15) and only a few points key to microbial eukaryotes are described below.

Genome structures

In addition to the diversity in genome sizes, microbial eukaryotes also have a variety of novel genome structures. Several of these structures, including extrachromosomal or subtelomeric rDNA genes, hypervariable karyotypes, and genome duality, appear to have arisen multiple times, whereas others, such as absolute strand polarity and highly-fragmented mitochondrial genomes, appear to be restricted to single lineages.

Mini- and maxicircles in the mitochondrial genomes of kinetoplastids

Kinetoplastids are defined by another unique genome feature that is found in their unusually structured mitochondria: kinetoplastid mitochondrial genomes exist as concatenated mini- and maxicircles 60, 61. Some of the maxicircles contain incomplete genes that require RNA editing to produce open reading frames, and at least part of the RNA editing is templated by sequences on minicircles [62]. The molecular mechanisms underlying the replication of these complex organellar genomes are still under

Summary

Our understanding of the tremendous diversity in genome size and structure in microbial eukaryotes stems from studies of relatively few eukaryotic lineages. Interpreting these studies in light of the current reconstruction of eukaryotic phylogeny indicates that some features have multiple origins, whereas others probably arose only once. Intriguingly, features that arose multiple times in eukaryotes, such as subtelomeric rDNAs and genome duality, are probably subject to some form of positive

Acknowledgements

This work is supported by two NSF grants (DEB-0092908 and DEB-0079325) to L.A.K.

Glossary

Glossary

Absolute strand polarity:
genes found in clusters on only a single strand of the DNA of kinetoplastids.
Conjugation:
a form of sex in which genetic material is transferred between two temporarily joined cells.
Episomal element:
small, extrachromosomal piece of DNA.
Genome duality:
the presence of two distinct types of genome (e.g. germline and somatic) within a given cell or organism.
Karyotype:
the complement of chromosomes within an organism; refers to both number and length of chromosomes.
Nucleomorph:

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