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 The rate of whole-genome duplication can be accelerated by hybridization

2020 ◽  
Author(s):  
S. Marsit ◽  
M. Hénault ◽  
G. Charron ◽  
A. Fijarczyk ◽  
C. R Landry
Keyword(s):  
Natural Selection ◽  
Genetic Variability ◽  
Genomic Instability ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Relaxed Selection ◽  
Confounding Effect ◽  
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 allows hybrids to thrive by 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. By measuring the spontaneous rate of WGD of 1304 yeast crosses evolved under relaxed selection, we show that some genotypes are more prone to WGD and WGD can be triggered by hybridization. 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 Spontaneous whole-genome duplication restores fertility in interspecific hybrids

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Guillaume Charron ◽  
Souhir Marsit ◽  
Mathieu Hénault ◽  
Hélène Martin ◽  
Christian R. Landry
Keyword(s):  
Interspecific Hybrids ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Cell ◽  
Whole Genome ◽  
Evolutionary Potential ◽  
Relaxed Selection ◽  
Interspecies Hybrids ◽  
Established Species ◽  
Fertility Recovery

Abstract Interspecies hybrids often show some advantages over parents but also frequently suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out genetic incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in species such as fungi that can also propagate asexually. Here, to test this, we evolve in parallel and under relaxed selection more than 600 diploid yeast inter-specific hybrids that span from 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occur in both hybrids between young and well-established species. Our results show that the instability of ploidy in hybrid is an accessible path to spontaneous fertility recovery.

scholarly journals Spontaneous whole-genome duplication restores fertility in interspecific hybrids

2019 ◽  
Author(s):  
Guillaume Charron ◽  
Souhir Marsit ◽  
Mathieu Hénault ◽  
Hélène Martin ◽  
Christian R. Landry
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Mitotic Cell ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Evolutionary Potential ◽  
Interspecies Hybrids ◽  
Ploidy Changes ◽  
Established Species ◽  
Fertility Recovery

AbstractInterspecies hybrids often show advantages over parents but suffer from reduced fertility, which can sometimes be overcome through sexual reproduction that sorts out incompatibilities. Sex is however inefficient due to the low viability or fertility of hybrid offspring and thus limits their evolutionary potential. Mitotic cell division could be an alternative to fertility recovery in facultative sexual species. To test this, we evolved under relaxed selection more than 600 diploid yeast hybrids between species that span 100,000 to 15 M years of divergence. We find that hybrids can recover fertility spontaneously and rapidly through whole-genome duplication. These events occurred in both hybrids between young and well-established species. Our results show that the instability of hybrid ploidy is a spontaneous path to fertility recovery.One Sentence SummaryPloidy changes potentiate hybrid speciation by leading to fertility recovery.

NAI2 and TSA1 Drive Differentiation of Constitutive and Inducible ER Body Formation in Brassicaceae

2019 ◽  
Vol 61 (4) ◽  
pp. 722-734 ◽  
Author(s):  
Natalia Stefanik ◽  
Jakub Bizan ◽  
Alwine Wilkens ◽  
Katarzyna Tarnawska-Glatt ◽  
Shino Goto-Yamada ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Transcription Factor ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Promoter Regions ◽  
Closely Related Species ◽  
Defense Strategies ◽  
Body Formation ◽  
Different Types

Abstract Brassicaceae and closely related species develop unique endoplasmic reticulum (ER)-derived structures called ER bodies, which accumulate β-glucosidases/myrosinases that are involved in chemical defense. There are two different types of ER bodies: ER bodies constitutively present in seedlings (cER bodies) and ER bodies in rosette leaves induced by treatment with the wounding hormone jasmonate (JA) (iER bodies). Here, we show that At-α whole-genome duplication (WGD) generated the paralogous genes NAI2 and TSA1, which consequently drive differentiation of cER bodies and iER bodies in Brassicaceae plants. In Arabidopsis, NAI2 is expressed in seedlings where cER bodies are formed, whereas TSA1 is expressed in JA-treated leaves where iER bodies are formed. We found that the expression of NAI2 in seedlings and the JA inducibility of TSA1 are conserved across other Brassicaceae plants. The accumulation of NAI2 transcripts in Arabidopsis seedlings is dependent on the transcription factor NAI1, whereas the JA induction of TSA1 in rosette leaves is dependent on MYC2, MYC3 and MYC4. We discovered regions of microsynteny, including the NAI2/TSA1 genes, but the promoter regions are differentiated between TSA1 and NAI2 genes in Brassicaceae. This suggests that the divergence of function between NAI2 and TSA1 occurred immediately after WGD in ancestral Brassicaceae plants to differentiate the formation of iER and cER bodies. Our findings indicate that At-α WGD enabled diversification of defense strategies, which may have contributed to the massive diversification of Brassicaceae plants.

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 Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

2017 ◽  
Author(s):  
Dei M. Elurbe ◽  
Sarita S. Paranjpe ◽  
Georgios Georgiou ◽  
Ila van Kruijsbergen ◽  
Ozren Bogdanovic ◽  
...  
Keyword(s):  
Xenopus Laevis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Regulatory Elements ◽  
Whole Genome ◽  
Dna Repeats ◽  
Vertebrate Genome ◽  
Closely Related Species ◽  
Flanking Regions ◽  
Regulatory Landscape

AbstractBackgroundGenome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. The most recent vertebrate genome duplication is that in Xenopus laevis, resulting from the hybridization of two closely related species about 17 million years ago [1]. However, little is known about the consequences of this duplication at the level of the genome, the epigenome and gene expression.ResultsOf the parental subgenomes, S chromosomes have degraded faster than L chromosomes ever since the genome duplication and until the present day. Deletions appear to have the largest effect on pseudogene formation and loss of regulatory regions. Deleted regions are enriched for long DNA repeats and the flanking regions have high alignment scores, suggesting that non-allelic homologous recombination (NAHR) has played a significant role in the loss of DNA. To assess innovations in the X. laevis subgenomes we examined p300 (Ep300)-bound enhancer peaks that are unique to one subgenome and absent from X. tropicalis. A large majority of new enhancers are comprised of transposable elements. Finally, to dissect early and late events following interspecific hybridization, we examined the epigenome and the enhancer landscape in X. tropicalis × X. laevis hybrid embryos. Strikingly, young X. tropicalis DNA transposons are derepressed and recruit p300 in hybrid embryos.ConclusionsThe results show that erosion of X. laevis genes and functional regulatory elements is associated with repeats and NAHR, and furthermore that young repeats have also contributed to the p300-bound regulatory landscape following hybridization and whole genome duplication.

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 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.

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