Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa

Science Advances, Год журнала: 2021, Номер 7(29)

Опубликована: Июль 1, 2021

Cannabis sativa has long been an important source of fiber extracted from hemp and both medicinal recreational drugs based on cannabinoid compounds. Here, we investigated its poorly known domestication history using whole-genome resequencing 110 accessions worldwide origins. We show that C. was first domesticated in early Neolithic times East Asia all current drug cultivars diverged ancestral gene pool currently represented by feral plants landraces China. identified candidate genes associated with traits differentiating cultivars, including branching pattern cellulose/lignin biosynthesis. also found evidence for loss function involved the synthesis two major biochemically competing cannabinoids during selection increased production or psychoactive properties. Our results provide a unique global view offer valuable genomic resources ongoing functional molecular breeding research.

Язык: Английский

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Effects of Synonymous Mutations beyond Codon Bias: The Evidence for Adaptive Synonymous Substitutions from Microbial Evolution Experiments

Genome Biology and Evolution, Год журнала: 2021, Номер 13(9)

Опубликована: Июнь 15, 2021

Synonymous mutations are often assumed to be neutral with respect fitness because they do not alter the encoded amino acid and so cannot "seen" by natural selection. Yet a growing body of evidence suggests that synonymous can have effects drive adaptive evolution through their impacts on gene expression protein folding. Here, we review what microbial experiments taught us about contribution adaptation. A survey site-directed mutagenesis reveals distributions for nonsynonymous more similar, especially beneficial mutations, than expected if all were neutral, suggesting should is typically observed. experimental studies where contributed adaptation shows impact range mechanisms including creation illicit RNA polymerase binding sites impacting transcription changes mRNA folding stability modulate translation. We suggest clonal interference in evolving populations may reason play smaller role based observed effects. finish discussing falsely assuming discuss directions future work exploring evolution.

Язык: Английский

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Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations

eLife, Год журнала: 2021, Номер 10

Опубликована: Янв. 19, 2021

Laboratory experimental evolution provides a window into the details of evolutionary process. To investigate consequences long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000 generations in three environments. We measured dynamics fitness changes over time, finding repeatable patterns declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with steady accumulation mutations, widespread genetic parallelism, historical contingency. In contrast to E. coli , do not observe coexistence or highly elevated mutation rates. find diploid involves both fixation heterozygous mutations frequent loss-of-heterozygosity events. Together, these results help distinguish aspects are likely be general features across many systems from those specific individual organisms environmental conditions.

Язык: Английский

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Evolutionary History of Plant Metabolism

Annual Review of Plant Biology, Год журнала: 2021, Номер 72(1), С. 185 - 216

Опубликована: Апрель 13, 2021

Tremendous chemical diversity is the hallmark of plants and supported by highly complex biochemical machinery. Plant metabolic enzymes originated were transferred from eukaryotic prokaryotic ancestors further diversified unprecedented rates gene duplication functionalization experienced in land plants. Unlike microbes, which have frequent horizontal transfer events multiple inputs energy organic carbon, predominantly rely on carbon generated CO2 very few, if any, transfers during their recent evolutionary history. As such, plant networks evolved a stepwise manner existing under various constraints. This review aims to take broader view evolution lay framework explore mechanisms network. Understanding underlying genetic constraints also an empirical prerequisite for rational engineering redesigning pathways.

Язык: Английский

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The population genomics of adaptive loss of function

Heredity, Год журнала: 2021, Номер 126(3), С. 383 - 395

Опубликована: Фев. 11, 2021

Abstract Discoveries of adaptive gene knockouts and widespread losses complete genes have in recent years led to a major rethink the early view that loss-of-function alleles are almost always deleterious. Today, surveys population genomic diversity revealing extensive content variation, yet significance much this variation remains unknown. Here we examine evolutionary dynamics loss function through lens genomics consider challenges opportunities studying using genetics models. We discuss how theoretically expected existence allelic heterogeneity, defined as multiple functionally analogous mutations at same locus, has proven consistent with empirical evidence why impedes both detection selection causal relationships phenotypes. then review technical progress towards new explicit tools genotype-phenotype methods overcome these limitations. More broadly, highlight value classifying way functional concept an allele from classical genetics.

Язык: Английский

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Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum

ISME Communications, Год журнала: 2024, Номер 4(1)

Опубликована: Янв. 1, 2024

Abstract Diatoms, a prominent group of phytoplankton, have significant impact on both the oceanic food chain and carbon sequestration, thereby playing crucial role in regulating climate. These highly diverse organisms show wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent vital source bioactive compounds that are widely used biotechnology applications. present study, we investigated genetic transcriptomic diversity 17 accessions model diatom Phaeodactylum tricornutum including those sampled century ago as well more recently collected accessions. The analysis data reveals higher emergence novel clades, indicating an increasing within P. population structure, compared previous study persistent long-term balancing selection genes old newly However, did not establish clear link between year sampling diversity, thereby, rejecting hypothesis loss heterozygoty cultured strains. Transcript identified transcript noncoding RNA other categories small such PiwiRNAs. Additionally, transcripts using differential expression Weighted Gene Correlation Network Analysis has provided evidence suppression or downregulation cannot be solely attributed loss-of-function mutations. This implies contributing factors, epigenetic modifications, may play gene expression. Our provides resources, which now accessible through platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), offer ease use advanced tools further investigate microalgae biology ecology, consequently enriching our current understanding these organisms.

Язык: Английский

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Adaptive gene loss in the common bean pan-genome during range expansion and domestication

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 7, 2024

Abstract The common bean ( Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild domesticated populations. Here, we present pan-genome based on five high-quality genomes whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% all presence/absence variants (PAVs). More non-synonymous mutations are found PAVs than core genes, probably reflecting lower effective population size fitness advantages due purging effect gene loss. Our results suggest shrinkage occurred during range expansion. Selection signatures provide evidence that partial or complete loss was key genetic change populations with major implications for plant adaptation. valuable resource food research breeding climate mitigation sustainable agriculture.

Язык: Английский

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Population genomics of premature termination codons in cavefish with substantial trait loss

Molecular Biology and Evolution, Год журнала: 2025, Номер unknown

Опубликована: Янв. 21, 2025

Abstract Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute adaptation. Cave-adapted organisms exhibit striking loss ancestral traits such as eyes and pigment, suggesting that loss-of-function may play an outsized role in these systems. Here, we leverage 141 whole genome sequences evaluate evolutionary history adaptive single nucleotide premature termination codons (PTCs) Mexican tetra. We find cave populations contain significantly more PTCs at high frequency than surface populations. also occur frequently genes inherent relaxed constraint relative rest genome. Using SLiM simulate PTC evolution cavefish population, show smaller population size increased drift is sufficient account for observed increase without positive selection. CRISPR-Cas9, mutation one genes, pde6c, produces phenotypes tetra mimic cave-derived traits. Finally, identify small subset candidate populations, within selective sweeps, beneficial reduced energy expenditure, handful be adaptive. Overall, our work provides rare characterization across wild finds they have important phenotypes, contributing growing body literature showing through subterranean organisms.

Язык: Английский

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Balanophora genomes display massively convergent evolution with other extreme holoparasites and provide novel insights into parasite–host interactions

Nature Plants, Год журнала: 2023, Номер 9(10), С. 1627 - 1642

Опубликована: Сен. 21, 2023

Язык: Английский

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Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Дек. 5, 2023

Abstract Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, cancer. The naked mole-rat ( Heterocephalus glaber ) contains abundant high-molecular-mass hyaluronic its tissues, contributes this species’ cancer resistance possibly longevity. Here we report that found wide range subterranean mammalian species, but not phylogenetically related aboveground species. These species accumulate by regulating the expression genes involved degradation synthesis contain unique mutations these genes. may benefit adaptation environment increasing skin elasticity protecting from oxidative stress due hypoxic conditions. Our work suggests has evolved with lifestyle.

Язык: Английский

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