Yeast genome evolution in the post-genome era

Seoighe, Cathal; Wolfe, Kenneth H.

doi:10.1016/s1369-5274(99)00015-6

Cited by 156 publications

(152 citation statements)

References 43 publications

Supporting

Mentioning

139

Contrasting

Unclassified

Order By: Relevance

“…High expression is therefore a genuine effect in duplicate retention, whether or not the protein belongs to a complex. This correlation has already been observed on a smaller scale in the yeast genome duplication 30 , indicating that it might be a general trait of WGD.…”

Section: Retention and Evolution Of Duplicate Genessupporting

confidence: 55%

“…4b). Most pathways are still significantly overamplified with respect to the recent duplication, an effect that has not been observed in WGDs analysed in other organisms 21,30 . As with protein complexes, the genes involved in a common metabolic pathway show a tendency to covary across the duplications, behaviour that can probably be attributed to stoichiometry, because imbalance in metabolic pathways may have a similar negative effect to that in multiprotein complexes.…”

Section: Retention and Evolution Of Duplicate Genesmentioning

confidence: 73%

“…Indeed, retention of duplicates for some of these genes, such as those encoding ribosome assembly proteins, is also observed in the WGDs of yeast and Arabidopsis 21,22,30 .…”

Section: Retention and Evolution Of Duplicate Genesmentioning

confidence: 98%

See 2 more Smart Citations

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

Aury

Jaillon

Duret

et al. 2006

Nature

761

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

Section: Retention and Evolution Of Duplicate Genessupporting

confidence: 55%

Section: Retention and Evolution Of Duplicate Genesmentioning

confidence: 73%

See 1 more Smart Citation

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

Aury

Jaillon

Duret

et al. 2006

Nature

761

836

View full text Add to dashboard Cite

show abstract

“…In addition to the discovery that WGD duplicated genes are functionally biased (Blanc and Wolfe, 2004;Seoighe and Gehring, 2004;Aury et al, 2006;Freeling, 2008;Wu et al, 2008;Schnable et al, 2009), several gene features were identified to associate with their retention probability, such as gene complexity (He and Zhang, 2005), gene length , essentiality (He and Zhang, 2006), expression level (Seoighe and Wolfe, 1999), evolutionary rates , number of protein interactions (Guan et al, 2007;Hakes et al, 2007), functional category (Blanc and Wolfe, 2004), alternative splicing status (Kopelman et al, 2005), protein structure (Papp et al, 2003;Liang et al, 2008), position in the protein-protein interaction network Wu and Qi, 2010), and number of phosphorylation sites (Amoutzias et al, 2010). However, it is unlikely that merely one or two features alone can account for the evolutionary process of duplicated genes, as many of these features are correlated to each other.…”

mentioning

confidence: 99%

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

et al. 2013

View full text Add to dashboard Cite

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.

show abstract

“…(d) TFs were more likely to be preserved in duplicate after WGD than genes in the genome at large An overabundance of surviving duplicated TFs after WGD was observed in several species (Blanc & Wolfe 2004;Maere et al 2005;Aury et al 2006), but not initially in yeast (Seoighe & Wolfe 1999). However, more recent work has confirmed that the WGD-produced duplicates are indeed enriched for TFs (Chen et al 2008;Conant & Wolfe 2008 (f) Duplicated TF genes may be slightly more dispensable than other TF genes Given the excess of shared target genes among the WGD TFs, it is reasonable to ask if the WGD-produced redundancy in target genes reduces the importance of these duplicated TFs in the regulatory network.…”

Section: Resultsmentioning

confidence: 99%

Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

Conant

2009

Proc. R. Soc. B.

View full text Add to dashboard Cite

I study the reorganization of the yeast transcriptional regulatory network after whole-genome duplication (WGD). Individual transcription factors (TFs) were computationally removed from the regulatory network, and the resulting networks were analysed. TF gene pairs that survive in duplicate from WGD show detectable redundancy as a result of that duplication. However, in most other respects, these duplicated TFs are indistinguishable from other TFs in the genome, suggesting that the duplicate TFs produced by WGD were rapidly diverted to distinct functional roles in the regulatory network. Separately, I find that genes targeted by many TFs appear to be preferentially retained in duplicate after WGD, an effect I attribute to selection to maintain dosage balance in the regulatory network after WGD.

show abstract

Yeast genome evolution in the post-genome era

Cited by 156 publications

References 43 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

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

Contact Info

Product

Resources

About