Domestication of Crop Metabolomes: Desired and Unintended Consequences

Trends in Plant Science, Journal Year: 2021, Volume and Issue: 26(6), P. 650 - 661

Published: Feb. 27, 2021

The majority of the crops and vegetables today were domesticated from their wild progenitors within past 12 000 years. Considerable research effort has been expended on characterizing genes undergoing positive negative selection during processes crop domestication improvement. Many studies have also documented how contents a handful metabolites altered human selection, but we are only beginning to unravel true extent metabolic consequences breeding. We highlight metabolomes wittingly or unwittingly shaped by domestication, can identify new targets for metabolite engineering purpose de novo relatives.

Language: Английский

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Evolutionary History of Plant Metabolism

Annual Review of Plant Biology, Journal Year: 2021, Volume and Issue: 72(1), P. 185 - 216

Published: April 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.

Language: Английский

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Analysis of the genetic loci of pigment pattern evolution in vertebrates

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2023, Volume and Issue: 98(4), P. 1250 - 1277

Published: April 5, 2023

ABSTRACT Vertebrate pigmentation patterns are amongst the best characterised model systems for studying genetic basis of adaptive evolution. The wealth available data on evolution allows analysis trends and quantitative testing evolutionary hypotheses. We employed Gephebase , a database variants associated with natural domesticated trait variation, to examine in how cis ‐regulatory coding mutations contribute vertebrate phenotypes, as well factors that favour one mutation type over other. found studies lower ascertainment bias identified higher proportions mutations, were more common animals harbouring number pigment cell classes. classified traits firstly according their physiological secondly whether they affect colour or pattern, carotenoid‐based variation pattern boundaries preferentially change. also genes developmental, cellular, molecular functions. greater proportion implicated upstream developmental processes compared those involved downstream cellular functions, ligands than respective receptors. Based these trends, we discuss future directions research

Language: Английский

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A large deletion at the cortex locus eliminates butterfly wing patterning

G3 Genes Genomes Genetics, Journal Year: 2022, Volume and Issue: 12(4)

Published: Jan. 31, 2022

Abstract As the genetic basis of natural and domesticated variation has been described in recent years, a number hotspot genes have repeatedly identified as targets selection, Heliconius butterflies display spectacular diversity pattern variants wild these patterns well-described. Here, we sought to identify mechanism behind an unusual variant that is instead found captivity, ivory mutant, which all scales on both wings body become white or yellow. Using combination autozygosity mapping coverage analysis from 37 captive individuals, 78-kb deletion at cortex wing patterning locus, gene associated with evolution H. melpomene 10 divergent lepidopteran species. This undetected among 458 genomes samples, its dosage explains homozygous heterozygous phenotypes captivity. The spans large 5′ region includes facultative 5′UTR exon detected larval disk transcriptomes. CRISPR mutagenesis this replicates coding knock-outs cortex, consistent functional role ivory-deleted elements establishing scale color fate. Population demographics reveal stock giving rise mutant mixed origin across range melpomene, supports scenario where mutation occurred after introduction haplotypes Ecuador. Homozygotes for are inviable while heterozygotes artificial joining 40 other examples allelic provide advantage animal populations under selection by fanciers breeders. Finally, our results highlight promise association identifying aberrant mutations insect populations.

Language: Английский

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Convergent evolution and predictability of gene copy numbers associated with diets in mammals

Genome Biology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Abstract Convergent evolution, the evolution of same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon nature. If genetic basis for convergent predictable to some extent, it may be possible infer organismic and capability organisms utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied association with relatively little known about potential contribution gene copy number changes. In this study, we explore whether particular families are linked diet shifts mammals assess if trophic ecology can inferred from numbers specific set families. Using 86 mammalian sequences, identified 24 trend toward higher herbivores, carnivores, omnivores, even after phylogenetic corrections. We were able confirm previous findings genes such as amylase, olfactory receptors, xenobiotic metabolism genes, identify novel whose correlate dietary patterns. For example, omnivores exhibited encoding regulators translation. also established discriminant function 13 that help predict extent. These highlight between families, suggesting develop method predicting animal

Language: Английский

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Detection of domestication signals through the analysis of the full distribution of fitness effects

Peer Community Journal, Journal Year: 2025, Volume and Issue: 5

Published: March 27, 2025

Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication are well documented, its basis-particularly dynamics selection-remain less understood. To investigate these dynamics, we performed simulations designed to approximate history large domestic mammals. These used selection coefficients as modeling tool represent in recognizing that such abstractions rather than direct representations biological reality. Specifically, analyzed site frequency spectra (SFS) under varying distributions fitness effects (DFE) proportions mutations with divergent pressures. Our results show discretized deleterious DFE can be reliably inferred from SFS single population, but reconstructing beneficial remains challenging, even when using joint both populations. We further developed novel inference model estimate proportion (p c), although found signals classic hard sweeps mimic increases p c, complicating interpretation. findings underscore utility limitations highlight need for caution interpreting histories domesticated populations based on assumptions.

Language: Английский

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The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies

Genes, Journal Year: 2021, Volume and Issue: 12(2), P. 184 - 184

Published: Jan. 27, 2021

Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation evolutionary dynamics tomato (R)-loci provides unique opportunities identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one most plastic diversified families. vast amount genomic data available Solanaceae wild relatives unprecedented insights into patterns mechanisms evolution NB-LRR genes. Comparative analysis remarked reshuffling R-islands on chromosomes high degree adaptive diversification key R-loci induced by species-specific pathogen pressure. Unveiling natural variation other species offers opportunity effectively exploit genetic diversity genomic-driven breeding programs with aim introducing new resistances cultivars. Within this motivating context, we reviewed repertoire genes improvement special focus signatures processes. This issue still relevant not thoroughly investigated. We believe discovery involved generation gene functions will bring great benefits future strategies.

Language: Английский

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Convergent copy number increase of genes associated with freshwater colonization in fishes

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1855)

Published: May 30, 2022

Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes which CNV important for adaptation novel environments. It also unclear whether same repeatedly change copy numbers adapting similar Here, we investigate associated with freshwater colonization fishes, was observed multiple times across different lineages. Using 48 ray-finned fishes diverse orders, identified 23 whose increases were colonization. These showed enrichment peptide receptor activity, hexosyltransferase activity unsaturated fatty metabolism. We further revealed that three populations compared marine ancestral stickleback genus Gasterosteus. results indicate involved metabolism (FADS2), immune function (PSMB8a) thyroid hormone (UGT2) may be at both inter-order macroevolutionary scale intra-genus microevolutionary scale. Further analysis taxa will help understand role This article part theme issue 'Genetic basis speciation: from loci causative mutations'.

Language: Английский

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Genetic basis of speciation and adaptation: from loci to causative mutations

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1855)

Published: May 30, 2022

Does evolution proceed in small steps or large leaps? How repeatable is evolution? constrained the evolutionary process? Answering these long-standing questions biology indispensable for both understanding how extant biodiversity has evolved and predicting organisms ecosystems will respond to changing environments future. Understanding genetic basis of phenotypic diversification speciation natural populations key properly answering questions. The leap forward genome sequencing technologies made it increasingly easier not only investigate architecture but also identify variant sites underlying adaptation populations. Furthermore, recent advances editing are making possible functions each candidate gene from In this article, we discuss technological enable analysis causative genes mutations such can help answer This article part theme issue ‘Genetic speciation: loci mutations’.

Language: Английский

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Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

Animals, Journal Year: 2021, Volume and Issue: 11(9), P. 2667 - 2667

Published: Sept. 10, 2021

Belyaev’s concept of destabilizing selection during domestication was a major achievement in the XX century. Its practical value has been realized commercial colors domesticated fox that never occur wild and confirmed wide variety pet breeds. Many human disease models involving animals allow to test drugs before testing. Perhaps this is why investigators doing transcriptomic profiling domestic versus have searched for breed-specific patterns. Here we sequenced hypothalamic transcriptomes tame aggressive rats, identified their differentially expressed genes (DEGs), and, first time, applied principal component analysis compare them with all known DEGs could find. Two components, PC1 PC2, respectively explained 67% 33% differential-gene-expression variance (hereinafter: log2 value) between animals. corresponded multiple orthologous supported by homologs; these kept sign from species tissue (i.e., common pattern). PC2 represented stand-alone homologous DEG pairs reversing one another representing intraspecific interspecific variation).

Language: Английский

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