scholarly journals Ectopic Gene Conversions in the Genome of Ten Hemiascomycete Yeast Species

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Robert T. Morris ◽  
Guy Drouin
Keyword(s):  
Gene Conversion ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Yeast Species ◽  
Whole Genome ◽  
Selective Pressures ◽  
Loss Of Introns ◽  
Gene Conversions

We characterized ectopic gene conversions in the genome of ten hemiascomycete yeast species. Of the ten species, three diverged prior to the whole genome duplication (WGD) event present in the yeast lineage and seven diverged after it. We analyzed gene conversions from three separate datasets: paralogs from the three pre-WGD species, paralogs from the seven post-WGD species, and common ohnologs from the seven post-WGD species. Gene conversions have similar lengths and frequency and occur between sequences having similar degrees of divergence, in paralogs from pre- and post-WGD species. However, the sequences of ohnologs are both more divergent and less frequently converted than those of paralogs. This likely reflects the fact that ohnologs are more often found on different chromosomes and are evolving under stronger selective pressures than paralogs. Our results also show that ectopic gene conversions tend to occur more frequently between closely linked genes. They also suggest that the mechanisms responsible for the loss of introns in S. cerevisiae are probably also involved in the gene 3'-end gene conversion bias observed between the paralogs of this species.

scholarly journals The neutral rate of whole-genome duplication varies among yeast species and their hybrids

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
S. Marsit ◽  
M. Hénault ◽  
G. Charron ◽  
A. Fijarczyk ◽  
C. R. Landry
Keyword(s):  
Natural Selection ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Yeast Species ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Relaxed Selection ◽  
Confounding Effect ◽  
Closely Related Species ◽  
Adaptive Mutations

AbstractHybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.

scholarly journals Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

2007 ◽  
Vol 104 (20) ◽  
pp. 8397-8402 ◽  
Author(s):  
D. R. Scannell ◽  
A. C. Frank ◽  
G. C. Conant ◽  
K. P. Byrne ◽  
M. Woolfit ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Yeast Species ◽  
Whole Genome ◽  
Gene Pairs

scholarly journals Evolutionary principles of modular gene regulation in yeasts

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Dawn A Thompson ◽  
Sushmita Roy ◽  
Michelle Chan ◽  
Mark P Styczynsky ◽  
Jenna Pfiffner ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Carbon Metabolism ◽  
Whole Genome Duplication ◽  
Time Course ◽  
Genome Duplication ◽  
Yeast Species ◽  
Substantial Contribution ◽  
Whole Genome ◽  
Phylogenetic Distance ◽  
Phylogenetic Framework

Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles.

scholarly journals Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning

2019 ◽  
Author(s):  
Daniel Escobar-Camacho ◽  
Karen L. Carleton ◽  
Devika W. Narain ◽  
Michele E.R. Pierotti
Keyword(s):  
Visual System ◽  
Gene Conversion ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Opsin Gene ◽  
Whole Genome ◽  
Gene Repertoire ◽  
Spectral Tuning ◽  
Diverse Range ◽  
System Evolution

AbstractVision represents an excellent model for studying adaptation, given the genotype-to-phenotype-map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we characterized the visual system of Neotropical Characiformes, which is the result of several spectral tuning mechanisms acting in concert including gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1/A2-chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform’s entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogs has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. In addition, characiforms exhibited species-specific differences in opsin expression. Finally, we found interspecific and intraspecific variation in the use of A1/A2-chromophores correlating with the light environment. These multiple mechanisms may be a result of the highly diverse visual environments where Characiformes have evolved.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

scholarly journals Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gareth B. Gillard ◽  
Lars Grønvold ◽  
Line L. Røsæg ◽  
Matilde Mengkrog Holen ◽  
Øystein Monsen ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Whole Genome Duplication ◽  
Genome Stability ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Doubling ◽  
Expression Evolution

Abstract Background Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago. Results We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. Conclusions Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.

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