Project description:Analysis of copy number variation in evolved haploid, diploid, tetraploid strains. All experimental samples were compared to the same reference strain S288C. The samples include the progenitor strains for the haploid, diploid, and tetraploid evolution experiments, and single colony isolates (clones) from the evolving populations at given time points. Evolved clones were analyzed at generation 250 unless the name is followed by gen35, gen55 or gen500, in which case those generations were analyzed.
Project description:Haploid, diploid, and tetraploid yeast were experimentally evolved in 2% raffinose medium. After 250 generations, we assessed the gene expression alterations in 2 evolved haploids, 2 evolved diploids, and 4 evolved tetraploids relative to the diploid ancestor.
Project description:Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through complex effects on the frequency or fitness of beneficial mutations. For example, in diverse cell types and organisms, immediately after a whole-genome duplication, newly formed polyploids missegregate chromosomes and undergo genetic instability. The instability following whole-genome duplications is thought to provide adaptive mutations in microorganisms and can promote tumorigenesis in mammalian cells. Polyploidy may also affect adaptation independently of beneficial mutations through ploidy-specific changes in cell physiology. Here we perform in vitro evolution experiments to test directly whether polyploidy can accelerate evolutionary adaptation. Compared with haploids and diploids, tetraploids undergo significantly faster adaptation. Mathematical modelling suggests that rapid adaptation of tetraploids is driven by higher rates of beneficial mutations with stronger fitness effects, which is supported by whole-genome sequencing and phenotypic analyses of evolved clones. Chromosome aneuploidy, concerted chromosome loss, and point mutations all provide large fitness gains. We identify several mutations whose beneficial effects are manifest specifically in the tetraploid strains. Together, these results provide direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.
Project description:Citrus, one of the world’s most important crops is facing considerable challenges due to drought events. Previous studies have demonstrated that tetraploid rootstocks exhibit greater tolerance to abiotic stresses than their diploid counterparts. The effects of combining tetraploid rootstock with a triploid scion under water deficit treatment have not been thoroughly explored. A water deficit experiment was conducted in pot using four citrus scion/rootstock combinations: diploid and tetraploid Swingle citrumelo rootstocks grafted with diploid Mexican Lime and triploid Persian lime. Physiological, biochemical, and transcriptomic analyses revealed that scions grafted onto tetraploid rootstocks had significantly better drought tolerance, especially when combined with triploid Persian lime. This improved resilience was linked to enhanced water regulation, higher photosynthesis, increased stomatal conductance and transpiration during water stress. Elevated abscisic acid levels and stronger antioxidant activity in polyploid rootstocks further contributed to stress response. Transcriptomic data showed notable gene expression changes, providing insights into drought tolerance mechanisms. These findings underscore ploidy’s role at both the rootstock and scion levels in shaping the plant’s response to water deficit, revealing useful interactions between rootstock and scion influencing drought resilience. This study highlights the potential for leveraging polyploid rootstocks and scions to improve drought tolerance in citrus cultivation.
Project description:Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy. Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (MATaaaa) strains.
Project description:Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy.
Project description:Strand specific RNA sequencing of S. pombe revealed a highly structured programme of ncRNA expression at over 600 loci. Waves of antisense transcription accompanied sexual differentiation. A substantial proportion of ncRNA arose from mechanisms previously considered to be largely artefactual, including improper 3’ termination and bi-directional transcription. Constitutive induction of the entire spk1+, spo4+, dis1+ and spo6+ antisense transcripts from an integrated, ectopic, locus disrupted their respective meiotic functions. This ability of antisense transcripts to disrupt gene function when expressed in trans suggests that cis production at native loci during sexual differentiation may also control gene function. Consistently, insertion of a marker gene adjacent to the dis1+ antisense start site mimicked ectopic antisense expression in reducing the levels of this microtubule regulator and abolishing the microtubule-dependent “horsetail” stage of meiosis. Antisense production had no impact at any of these loci when the RNAi machinery was removed. Thus, far from being simply ‘genome chatter’, this extensive ncRNA landscape constitutes a fundamental component in the controls that drive the complex programme of sexual differentiation in S. pombe. Thorough interrogation of the Schizosaccharomyces pombe transcriptome during sexual differentiation using strand-specific total RNA sequencing (AB SOLiD 3.0 and 3.0+). A total of 19 samples were analysed by two separate machine runs (henceforth first and second runs, respectively). In the first machine run the following 5 samples were processed (on a single sequencing slide): Vegetative haploid (strain IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following temperature shift from 25ºC to 32ºC to induce meiosis by Pat1 inactivation. In the second machine run the following 14 samples were processed (on two sequencing slides): Vegetative haploid (IH5974), pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift (a biological replicate of the first machine run). In addition, asynchronous IH3365 (wild type diploid) was also sequenced to enable a series of pair-wise haploid/diploid comparisons between itself, asynchronous haploid (IH5974) and pat1.114 diploid (IH2912) at vegetative growth. Finally, to find putative targets of the two bzip transcription factors atf21 and atf31, we sequenced RNA extracts from IH8832 (atf21.delta diploid) and IH8814 (atf31.delta diploid) before (0), and 3, 5, and 10 hours after the temperature shift, while the pat1.114 diploid (IH2912) at vegetative growth (0) and pat1.114 diploid (IH2912) at 3, 5 and 10 hours following the temperature shift were used as reference for this analysis.