Genome Remodeling in Ciliated Protozoa

Jahn, Carolyn L.; Klobutcher, Lawrence A.

doi:10.1146/annurev.micro.56.012302.160916

Cited by 172 publications

(157 citation statements)

References 143 publications

Supporting

Mentioning

151

Contrasting

Unclassified

Order By: Relevance

“…Ciliates are unique among unicellular organisms in that they separate germline and somatic functions 1 . Each cell harbours two kinds of nucleus, namely silent diploid micronuclei and highly polyploid macronuclei.…”

mentioning

confidence: 99%

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Aury

Jaillon

Duret

et al. 2006

Nature

763

836

View full text Add to dashboard Cite

The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Phylogenetic analysis indicates that the most recent duplication coincides with an explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species. We observed that gene loss occurs over a long timescale, not as an initial massive event. Genes from the same metabolic pathway or protein complex have common patterns of gene loss, and highly expressed genes are over-retained after all duplications. The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints.Ciliates are unique among unicellular organisms in that they separate germline and somatic functions 1 . Each cell harbours two kinds of nucleus, namely silent diploid micronuclei and highly polyploid macronuclei. The latter are unusual in that they contain an extensively rearranged genome streamlined for expression and divide by a non-mitotic process. Only micronuclei undergo meiosis to perpetuate genetic information; the macronuclei are lost at each sexual generation and develop anew from the micronuclear lineage.In Paramecium the exact number of micronuclear chromosomes (more than 50) and the structures of their centromeres and telomeres remain unknown. During macronuclear development, these chromosomes are amplified to about 800 copies and undergo two types of DNA elimination event. Tens of thousand of short, unique copy elements (internal eliminated sequences) are removed by a precise mechanism that leads to the reconstitution of functional genes 2 .Transposable elements and other repeated sequences are removed by an imprecise mechanism leading either to chromosome fragmentation and de novo telomere addition or to variable internal deletions 3 . These rearrangements occur after a few rounds of endoreplication, leading to some heterogeneity in the sequences abutting the imprecisely eliminated regions 3 . The sizes of the resulting, acentric macronuclear chromosomes range from 50-1,000 kilobases (kb) as measured by pulsed-field gel electrophoresis. Because the sexual process of autogamy results in an entirely homozygous genotype 4 , the macronuclear DNA that was sequenced was genetically homogeneous.The Paramecium genome sequence The Paramecium macronuclear genome sequence was established with the use of a whole-genome shotgun and assembly strategy. Paired-end sequencing of plasmid and bacterial artificial chromosome (BAC) clones provided a coverage of 13 genome equivalents (Supplementary Table S1). We assembled the sequence reads with Arachne 5 in 1,907 contigs connected in 697 scaffolds of size greater than 2 kb, giving a total coverage of 72...

show abstract

mentioning

confidence: 99%

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Aury

Jaillon

Duret

et al. 2006

Nature

763

836

View full text Add to dashboard Cite

show abstract

“…Others such as Toxoplasma gondii, Cryptosporidium parvum, and C. hominis are primarily health threats in HIVϩ/AIDS and immunosuppressed populations (7). Ciliates are unique among unicellular organisms in that they separate germline and somatic functions (8).…”

mentioning

confidence: 99%

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Martens

Vandepoele

Peer

2008

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The chromalveolates form a highly diverse and fascinating assemblage of organisms, ranging from obligatory parasites such as Plasmodium to free-living ciliates and algae such as kelps, diatoms, and dinoflagellates. Many of the species in this monophyletic grouping are of major medical, ecological, and economical importance. Nevertheless, their genome evolution is much less well studied than that of higher plants, animals, or fungi. In the current study, we have analyzed and compared 12 chromalveolate species for which wholesequence information is available and provide a detailed picture on gene loss and gene gain in the different lineages. As expected, many gene loss and gain events can be directly correlated with the lifestyle and specific adaptations of the organisms studied. For instance, in the obligate intracellular Apicomplexa we observed massive loss of genes that play a role in general basic processes such as amino acid, carbohydrate, and lipid metabolism, reflecting the transition of a free-living to an obligate intracellular lifestyle. In contrast, many gene families show species-specific expansions, such as those in the plant pathogen oomycete Phytophthora that are involved in degrading the plant cell wall polysaccharides to facilitate the pathogen invasion process. In general, chromalveolates show a tremendous difference in genome structure and evolution and in the number of genes they have lost or gained either through duplication or horizontal gene transfer.gene gain ͉ gene loss

show abstract

“…The process continues until all MDSs have been assembled. For details related to ciliates and gene assembly we refer to [16], [21], [22], [23], [24], [25], [26], [27]. For details related to the intramolecular model and its mathematical formalizations we refer to [4], [5], [8], [9], [13], [14], [15], [29], [30], as well as to the recent monograph [6].…”

Section: Introductionmentioning

confidence: 99%

Modelling Simple Operations for Gene Assembly

Harju

Petre

Rozenberg

Natural Computing Series

View full text Add to dashboard Cite

Summary. The intramolecular model ) for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any micronuclear gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and may consist of many coding and non-coding blocks. We consider in this paper some restricted variants of the three operations, where only one coding block is rearranged at a time. We present in this paper the molecular model of these simple operations. We also introduce a mathematical model for the simple operations, on three levels of abstractions: MDS descriptors, signed permutations, and signed double occurrence strings. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful strategy.

show abstract

Genome Remodeling in Ciliated Protozoa

Cited by 172 publications

References 143 publications

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

Modelling Simple Operations for Gene Assembly

Contact Info

Product

Resources

About