scholarly journals The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations

2021 ◽  
Author(s):  
Sudipta Tung ◽  
Christopher W. Bakerlee ◽  
Angela M. Phillips ◽  
Alex N. Nguyen Ba ◽  
Michael M. Desai
Keyword(s):  
Genome Stability ◽  
Genetic Basis ◽  
Budding Yeast ◽  
Whole Genome ◽  
Laboratory Evolution ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Wild Strains ◽  
Potential Strategy ◽  
Functional Copy

ABSTRACTSpontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains ofSaccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in theSSD1gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains ofS. cerevisiaeto show that clonal populations of strains with a functional copy ofSSD1autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.

scholarly journals The Genetic Basis of Differential Autodiploidization in Evolving Yeast Populations

2021 ◽  
Author(s):  
Sudipta Tung ◽  
Christopher W Bakerlee ◽  
Angela M Phillips ◽  
Alex N Nguyen Nguyen Ba ◽  
Michael M Desai
Keyword(s):  
Genome Stability ◽  
Genetic Basis ◽  
Budding Yeast ◽  
Whole Genome ◽  
Laboratory Evolution ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Wild Strains ◽  
Potential Strategy ◽  
Functional Copy

Abstract Spontaneous whole-genome duplication, or autodiploidization, is a common route to adaptation in experimental evolution of haploid budding yeast populations. The rate at which autodiploids fix in these populations appears to vary across strain backgrounds, but the genetic basis of these differences remains poorly characterized. Here we show that the frequency of autodiploidization differs dramatically between two closely related laboratory strains of Saccharomyces cerevisiae, BY4741 and W303. To investigate the genetic basis of this difference, we crossed these strains to generate hundreds of unique F1 segregants and tested the tendency of each segregant to autodiplodize across hundreds of generations of laboratory evolution. We find that variants in the SSD1 gene are the primary genetic determinant of differences in autodiploidization. We then used multiple laboratory and wild strains of S. cerevisiae to show that clonal populations of strains with a functional copy of SSD1 autodiploidize more frequently in evolution experiments, while knocking out this gene or replacing it with the W303 allele reduces autodiploidization propensity across all genetic backgrounds tested. These results suggest a potential strategy for modifying rates of spontaneous whole-genome duplications in laboratory evolution experiments in haploid budding yeast. They may also have relevance to other settings in which eukaryotic genome stability plays an important role, such as biomanufacturing and the treatment of pathogenic fungal diseases and cancers.

scholarly journals Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome

Nature Plants ◽  
2021 ◽  
Author(s):  
Liuyu Qin ◽  
Yiheng Hu ◽  
Jinpeng Wang ◽  
Xiaoliang Wang ◽  
Ran Zhao ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Sequence Data ◽  
Expression Patterns ◽  
Whole Genome ◽  
Angiosperm Evolution ◽  
Aristolochic Acids ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
High Quality Genome ◽  
Angiosperm Genome

AbstractAristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

scholarly journals On the Expansion of “Dangerous” Gene Repertoires by Whole-Genome Duplications in Early Vertebrates

Cell Reports ◽  
2012 ◽  
Vol 2 (5) ◽  
pp. 1387-1398 ◽  
Author(s):  
Param Priya Singh ◽  
Séverine Affeldt ◽  
Ilaria Cascone ◽  
Rasim Selimoglu ◽  
Jacques Camonis ◽  
...  
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Early Vertebrates

scholarly journals Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 563 ◽  
Author(s):  
Anna Szczepaniak ◽  
Michał Książkiewicz ◽  
Jan Podkowiński ◽  
Katarzyna Czyż ◽  
Marek Figlerowicz ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Coenzyme A ◽  
Phylogenetic Inference ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Acetyl Coenzyme A Carboxylase

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

scholarly journals Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

2018 ◽  
Vol 221 (1) ◽  
pp. 565-576 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
André M. Amorim ◽  
M. Sugumaran ◽  
Joshua S. Rest ◽  
...  
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications
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