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1.
PLoS Biol ; 18(8): e3000757, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32833957

RESUMO

In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation ("nutrient-growth dysregulation") can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine-auxotrophic mutant lys- encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A subpopulation repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). Organosulfurs, mainly reduced glutathione (GSH) and GSH conjugates, were released by lys- cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys-orgS- by eliciting a proper slow growth program, including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.


Assuntos
Adaptação Fisiológica/genética , Lisina/farmacologia , Redes e Vias Metabólicas/efeitos dos fármacos , Nutrientes/farmacologia , Saccharomyces cerevisiae/metabolismo , Autofagia/efeitos dos fármacos , Autofagia/genética , Evolução Biológica , Glucose/metabolismo , Glucose/farmacologia , Lisina/deficiência , Redes e Vias Metabólicas/genética , Nitrogênio/metabolismo , Nitrogênio/farmacologia , Nutrientes/metabolismo , Ribossomos/efeitos dos fármacos , Ribossomos/metabolismo , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Sirolimo/farmacologia , Estresse Fisiológico
2.
Am J Hum Genet ; 107(3): 473-486, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32781046

RESUMO

Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.


Assuntos
Adaptação Fisiológica/genética , Variação Genética/genética , Seleção Genética/genética , Pigmentação da Pele/genética , Grupo com Ancestrais do Continente Africano/genética , Antiporters/genética , Gerenciamento de Dados , Etiópia/epidemiologia , Feminino , Genética Populacional , Genoma Humano/genética , Haplótipos/genética , Humanos , Masculino , Glicoproteínas de Membrana/genética , Oxirredutases/genética , Polimorfismo de Nucleotídeo Único/genética , Nexinas de Classificação/genética , Proteínas Supressoras de Tumor/genética , Uganda/epidemiologia
3.
Science ; 369(6501)2020 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-32675347

RESUMO

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.


Assuntos
Adaptação Fisiológica/genética , Antozoários/genética , Genoma , Animais , Recifes de Corais , Genética Populacional , Estudo de Associação Genômica Ampla , Genômica
4.
PLoS Pathog ; 16(7): e1008700, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32687537

RESUMO

With antibiotic resistance rates on the rise, it is critical to understand how microbial species interactions influence the evolution of resistance. In obligate mutualisms, the survival of any one species (regardless of its intrinsic resistance) is contingent on the resistance of its cross-feeding partners. This sets the community antibiotic sensitivity at that of the 'weakest link' species. In this study, we tested the hypothesis that weakest link dynamics in an obligate cross-feeding relationship would limit the extent and mechanisms of antibiotic resistance evolution. We experimentally evolved an obligate co-culture and monoculture controls along gradients of two different antibiotics. We measured the rate at which each treatment increased antibiotic resistance, and sequenced terminal populations to question whether mutations differed between mono- and co-cultures. In both rifampicin and ampicillin treatments, we observed that resistance evolved more slowly in obligate co-cultures of E. coli and S. enterica than in monocultures. While we observed similar mechanisms of resistance arising under rifampicin selection, under ampicillin selection different resistance mechanisms arose in co-cultures and monocultures. In particular, mutations in an essential cell division protein, ftsI, arose in S. enterica only in co-culture. A simple mathematical model demonstrated that reliance on a partner is sufficient to slow the rate of adaptation, and can change the distribution of adaptive mutations that are acquired. Our results demonstrate that cooperative metabolic interactions can be an important modulator of resistance evolution in microbial communities.


Assuntos
Adaptação Fisiológica/efeitos dos fármacos , Resistência Microbiana a Medicamentos/fisiologia , Escherichia coli/fisiologia , Interações Microbianas/fisiologia , Salmonella enterica/fisiologia , Adaptação Fisiológica/genética , Ampicilina/farmacologia , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Técnicas de Cocultura , Escherichia coli/efeitos dos fármacos , Interações Microbianas/efeitos dos fármacos , Modelos Teóricos , Mutação , Rifampina/farmacologia , Salmonella enterica/efeitos dos fármacos
5.
PLoS Genet ; 16(7): e1008882, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32673315

RESUMO

Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas.


Assuntos
Adaptação Fisiológica/genética , Florígeno/metabolismo , Proteínas de Plantas/genética , Zea mays/genética , Aclimatação/genética , Temperatura Baixa , Flores/genética , Flores/crescimento & desenvolvimento , Humanos , Fotoperíodo , Proteínas de Plantas/metabolismo , Locos de Características Quantitativas/genética , Zea mays/crescimento & desenvolvimento
6.
Nat Commun ; 11(1): 3676, 2020 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-32719321

RESUMO

The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.


Assuntos
Mapeamento Cromossômico , Cromossomos/genética , Evolução Molecular , Poríferos/genética , Adaptação Fisiológica/genética , Animais , Epigênese Genética , Água Doce , Regulação da Expressão Gênica no Desenvolvimento , Anotação de Sequência Molecular , Filogenia , Poríferos/crescimento & desenvolvimento , RNA-Seq , Análise de Sequência de DNA , Sintenia
7.
PLoS One ; 15(7): e0235397, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32628713

RESUMO

Appropriate flowering and maturity time are important for soybean production. Four maturity genes E1, E2, E3 and E4 have been molecularly identified and found to play major roles in the control of flowering and maturity of soybean. Here, to further investigate the effect of different allele combinations of E1-E4, we performed Kompetitive Allele Specific PCR (KASP) assays based on single nucleotide polymorphisms (SNPs) at these four E loci, and genotyped E1-E4 genes across 308 Chinese cultivars with a wide range of maturity groups. In total, twenty-one allele combinations for E1-E4 genes were identified across these Chinese cultivars. Various combinations of mutations at four E loci gave rise to the diversity of flowering and maturity time, which were associated with the adaptation of soybean cultivars to diverse geographic regions and farming systems. In particular, the cultivars with mutations at all four E loci reached flowering and maturity very early, and adapted to high-latitude cold regions. The allele combinations e1-as/e2-ns/e3-tr/E4, E1/e2-ns/E3/E4 and E1/E2/E3/E4 played important roles in the Northeast China, Huang-Huai-Hai (HHH) Rivers Valley and South China regions, respectively. Notably, E1 and E2, especially E2, affected flowering and maturity time of soybean significantly. Our study will be beneficial for germplasm evaluation, cultivar improvement and regionalization of cultivation in soybean production.


Assuntos
Adaptação Fisiológica/genética , Regulação da Expressão Gênica de Plantas , Genes Controladores do Desenvolvimento , Locos de Características Quantitativas , Soja/fisiologia , Alelos , China , Produção Agrícola , Fazendas , Flores/crescimento & desenvolvimento , Genes de Plantas , Variação Genética , Genótipo , Geografia , Fotoperíodo , Fatores de Tempo
8.
Proc Natl Acad Sci U S A ; 117(29): 17112-17121, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32647058

RESUMO

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.


Assuntos
Adaptação Fisiológica/genética , Mudança Climática , Ecossistema , Temperatura Alta , Animais , Austrália , Clima Desértico , Ecótipo , Peixes/genética , Peixes/fisiologia , Genômica , Transcriptoma/genética
9.
Trends Ecol Evol ; 35(10): 897-907, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32674869

RESUMO

Evolutionary ecological theory suggests that selection arising from interactions with conspecifics, such as sexual and kin selection, may result in evolution of intraspecific conflicts and evolutionary 'tragedy of the commons'. Here, we propose that such an evolution of conspecific conflicts may affect population dynamics in a way that enhances species coexistence. Empirical evidence and theoretical models suggest that more abundant species is more susceptible to invasion of 'selfish' individuals that increase their own reproductive success at the expense of population growth (intraspecific adaptation load). The density-dependent intraspecific adaptation load gives rise to a self-regulation mechanism at the population level, and stabilizes species coexistence at the community level by negative frequency-dependence.


Assuntos
Adaptação Fisiológica , Evolução Biológica , Aclimatação , Adaptação Fisiológica/genética , Humanos , Dinâmica Populacional , Reprodução
10.
Nat Commun ; 11(1): 3320, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620776

RESUMO

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer insights into the genetic diversity and gene functions in benthic diatoms.


Assuntos
Adaptação Fisiológica/genética , Diatomáceas/genética , Ecossistema , Evolução Molecular , Genoma/genética , Diatomáceas/classificação , Diatomáceas/metabolismo , Água Doce , Tamanho do Genoma , Genômica/métodos , Polimorfismo de Nucleotídeo Único , Água do Mar , Especificidade da Espécie , Transcriptoma/genética
11.
Mol Genet Genomics ; 295(6): 1401-1414, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32661592

RESUMO

Plants respond to the environmental perturbations by triggering the dynamic changes within the transcriptome. The assessment of these oscillations within the transcriptome would offer insights into the ecological adaptation of the plants. We evaluated how the transcriptome of Taxus contorta swings under natural conditions to elucidate its adaptive response. Thus, our study provides new insights into the performance of T. contorta under a changing environment during different seasons. The abundance estimation using the RNAseq approach revealed 6727 differentially expressed genes. Comprehensive reprogramming was observed in Taxol biosynthesis, maintenance of redox homeostasis, and generation of effective shield to UV-B, high light intensity, and temperature. Besides differential expression, the alternative splicing (AS) and single nucleotide variations (SNVs) also confer flexibility to the transcriptome of T. contorta. 1936 differentially expressing transcripts were also found to exhibit Differential Exon Usage (DEU) as well as differential SNVs. LC-MS-based untargeted metabolic analysis revealed 7774 ion features, among which around 334 putatively identified metabolites were differentially regulated. Our results showed that the swing and the oscillations of the transcriptome and metabolome of T. contorta ensure adaptability and better survival under changing environment. In addition, varying patterns of AS and SNVs compliment the adaptation provided by differential expression.


Assuntos
Adaptação Fisiológica/genética , Reprogramação Celular , Proteínas de Plantas/metabolismo , Polimorfismo de Nucleotídeo Único , Taxus/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Taxus/classificação , Taxus/genética , Taxus/crescimento & desenvolvimento
12.
Proc Natl Acad Sci U S A ; 117(29): 17438-17445, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32636259

RESUMO

Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.


Assuntos
Adaptação Fisiológica/genética , Clorófitas/genética , Clorófitas/fisiologia , Dessecação , Regulação da Expressão Gênica de Plantas , Clorofíceas/genética , Clorofíceas/fisiologia , Regulação para Baixo , Extremófilos/fisiologia , Ontologia Genética , Genes de Plantas/genética , Fatores de Transcrição , Transcriptoma , Regulação para Cima
13.
PLoS One ; 15(7): e0236571, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730284

RESUMO

The occurrence of genotype by environment interaction (G x E), which is defined as the differential response of genotypes to environmental variation, is frequently reported in maize cultures, making it challenging to recommend cultivars. Methods allowing to study the potential nonlinear pattern of genotype responses to environmental variation allied to prior beliefs on unknown parameters are interesting to evaluate the phenotypic adaptability and stability of genotypes. In this context, the present study aimed to assess the adaptability and stability of maize hybrids, by using the Bayesian segmented regression model, and evaluate the efficacy of using informative and minimally informative prior distributions for the selection of cultivars. Randomized complete-block design experiments were carried out to study the yield (kg/ha) of 25 maize hybrids, in 22 different environments, in Northeastern Brazil. The Bayesian segmented regression model fitted using informative prior distributions presented lower credibility intervals and Deviance Criterium of Information values, compared to those obtained by fitting using minimally informative distributions. Therefore, the model using informative prior distributions was considered for the adaptability and stability evaluation of maize genotypes. Once most northeastern farmers in Brazil have limited capital, the genotype P4285HX should be considered for planting, due to its high yield performance and adaptability to unfavorable environments.


Assuntos
Modelos Genéticos , Zea mays/genética , Adaptação Fisiológica/genética , Teorema de Bayes , Interação Gene-Ambiente , Genótipo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Zea mays/crescimento & desenvolvimento , Zea mays/metabolismo
14.
PLoS One ; 15(7): e0234550, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32663226

RESUMO

Chickpea has a profound nutritional and economic value in vegetarian society. Continuous decline in chickpea productivity is attributed to insufficient genetic variability and different environmental stresses. Chickpea like several other legumes is highly susceptible to terminal drought stress. Multiple genes control drought tolerance and ASR gene plays a key role in regulating different plant stresses. The present study describes the molecular characterization and functional role of Abscissic acid and stress ripening (ASR) gene from chickpea (Cicer arietinum) and the gene sequence identified was submitted to NCBI Genbank (MK937569). Molecular analysis using MUSCLE software proved that the ASR nucleotide sequences in different legumes show variations at various positions though ASR genes are conserved in chickpea with only few variations. Sequence similarity of ASR gene to chickpea putative ABA/WDS induced protein mRNA clearly indicated its potential involvement in drought tolerance. Physiological screening and qRT-PCR results demonstrated increased ASR gene expression under drought stress possibly enabled genotypes to perform better under stress. Conserved domain search, protein structure analysis, prediction and validation, network analysis using Phyre2, Swiss-PDB viewer, ProSA and STRING analysis established the role of hypothetical ASR protein NP_001351739.1 in mediating drought responses. NP_001351739.1 might have enhanced the ASR gene activity as a transcription factor regulating drought stress tolerance in chickpea. This study could be useful in identification of new ASR genes that play a major role in drought tolerance and also develop functional markers for chickpea improvement.


Assuntos
Cicer/genética , Regulação da Expressão Gênica de Plantas/genética , Estresse Fisiológico/genética , Ácido Abscísico/farmacologia , Adaptação Fisiológica/genética , Sequência de Bases/genética , Cicer/crescimento & desenvolvimento , Secas , Perfilação da Expressão Gênica/métodos , Genótipo , Proteínas de Plantas/genética , Raízes de Plantas/metabolismo , Fatores de Transcrição/metabolismo
15.
Nat Rev Endocrinol ; 16(9): 519-533, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32620937

RESUMO

Reproductive function adjusts in response to environmental conditions in order to optimize success. In humans, this plasticity includes age of pubertal onset, hormone levels and age at menopause. These reproductive characteristics vary across populations with distinct lifestyles and following specific childhood events, and point to a role for the early-life environment in shaping adult reproductive trajectories. Epigenetic mechanisms respond to external signals, exert long-term effects on gene expression and have been shown in animal and cellular studies to regulate normal reproductive function, strongly implicating their role in these adaptations. Moreover, human cohort data have revealed differential DNA methylation signatures in proxy tissues that are associated with reproductive phenotypic variation, although the cause-effect relationships are difficult to discern, calling for additional complementary approaches to establish functionality. In this Review, we summarize how adult reproductive function can be shaped by childhood events. We discuss why the influence of the childhood environment on adult reproductive function is an important consideration in understanding how reproduction is regulated and necessitates consideration by clinicians treating women with diverse life histories. The resolution of the molecular mechanisms responsible for human reproductive plasticity could also lead to new approaches for intervention by targeting these epigenetic modifications.


Assuntos
Adaptação Fisiológica/genética , Meio Ambiente , Epigênese Genética/fisiologia , Reprodução/genética , Envelhecimento , Animais , Metilação de DNA , Feminino , Fertilidade , Desenvolvimento Fetal , Humanos , Estilo de Vida , Masculino , Fenômenos Fisiológicos da Nutrição Materna , Fenótipo , Gravidez , Progesterona/sangue , Puberdade/genética , Reprodução/fisiologia , Testosterona/sangue , Migrantes
16.
Science ; 368(6498): 1495-1499, 2020 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-32587022

RESUMO

Although sled dogs are one of the most specialized groups of dogs, their origin and evolution has received much less attention than many other dog groups. We applied a genomic approach to investigate their spatiotemporal emergence by sequencing the genomes of 10 modern Greenland sled dogs, an ~9500-year-old Siberian dog associated with archaeological evidence for sled technology, and an ~33,000-year-old Siberian wolf. We found noteworthy genetic similarity between the ancient dog and modern sled dogs. We detected gene flow from Pleistocene Siberian wolves, but not modern American wolves, to present-day sled dogs. The results indicate that the major ancestry of modern sled dogs traces back to Siberia, where sled dog-specific haplotypes of genes that potentially relate to Arctic adaptation were established by 9500 years ago.


Assuntos
Adaptação Fisiológica/genética , Cães/genética , Animais , Apolipoproteínas/genética , Regiões Árticas , Ácidos Graxos/metabolismo , Genoma , Groenlândia , Haplótipos , Proteínas de Transporte da Membrana Mitocondrial/genética , Seleção Artificial , Análise de Sequência de DNA , Sibéria , Triglicerídeos/metabolismo , Lobos/genética
17.
Science ; 368(6495): 1127-1131, 2020 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-32499442

RESUMO

In microorganisms, evolutionarily conserved mechanisms facilitate adaptation to harsh conditions through stress-induced mutagenesis (SIM). Analogous processes may underpin progression and therapeutic failure in human cancer. We describe SIM in multiple in vitro and in vivo models of human cancers under nongenotoxic drug selection, paradoxically enhancing adaptation at a competing intrinsic fitness cost. A genome-wide approach identified the mechanistic target of rapamycin (MTOR) as a stress-sensing rheostat mediating SIM across multiple cancer types and conditions. These observations are consistent with a two-phase model for drug resistance, in which an initially rapid expansion of genetic diversity is counterbalanced by an intrinsic fitness penalty, subsequently normalizing to complete adaptation under the new conditions. This model suggests synthetic lethal strategies to minimize resistance to anticancer therapy.


Assuntos
Adaptação Fisiológica/genética , Antineoplásicos/farmacologia , Resistencia a Medicamentos Antineoplásicos/genética , Mutagênese , Neoplasias/tratamento farmacológico , Neoplasias/genética , Serina-Treonina Quinases TOR/metabolismo , Antineoplásicos/uso terapêutico , Linhagem Celular Tumoral , Reparo do DNA/genética , Aptidão Genética , Estudo de Associação Genômica Ampla , Humanos , Seleção Genética , Transdução de Sinais , Serina-Treonina Quinases TOR/genética
18.
Nat Commun ; 11(1): 2885, 2020 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-32514036

RESUMO

The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures of selection, indicating polygenic selection. We isolate the gene REDUCED POLLEN NUMBER1 (RDP1) at the locus with the strongest association. We validate its effect using a quantitative complementation test with CRISPR/Cas9-generated null mutants in nonstandard wild accessions. In contrast to pleiotropic null mutants, only pollen numbers are significantly affected by natural allelic variants. These data support theoretical predictions that reduced investment in male gametes is advantageous in predominantly selfing species.


Assuntos
Adaptação Fisiológica/genética , Arabidopsis/genética , Genes de Plantas/genética , Pólen/genética , Arabidopsis/metabolismo , Sequência de Bases , Sistemas CRISPR-Cas/genética , Evolução Molecular , Mutação , Plantas Geneticamente Modificadas , Pólen/citologia , Pólen/metabolismo , Reprodução/genética , Homologia de Sequência do Ácido Nucleico
19.
Genet Sel Evol ; 52(1): 33, 2020 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-32591011

RESUMO

BACKGROUND: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krskopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. RESULTS: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. CONCLUSIONS: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.


Assuntos
Técnicas de Genotipagem/métodos , Seleção Genética/genética , Suínos/genética , Aclimatação/genética , Adaptação Fisiológica/genética , Algoritmos , Animais , Cruzamento , Domesticação , Europa (Continente) , Feminino , Genoma/genética , Genômica/métodos , Genótipo , Masculino , Modelos Genéticos , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Sequenciamento Completo do Genoma/métodos
20.
PLoS One ; 15(6): e0234721, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579573

RESUMO

Systems biology based approaches have been effectively utilized to mine high throughput data. In the current study, we have performed system-level analysis for Deinococcus radiodurans R1 by constructing a gene co-expression network based on several microarray datasets available in the public domain. This condition-independent network was constructed by Weighted Gene Co-expression Network Analysis (WGCNA) with 61 microarray samples from 9 different experimental conditions. We identified 13 co-expressed modules, of which, 11 showed functional enrichments of one or more pathway/s or biological process. Comparative analysis of differentially expressed genes and proteins from radiation and desiccation stress studies with our co-expressed modules revealed the association of cyan with radiation response. Interestingly, two modules viz darkgreen and tan was associated with radiation as well as desiccation stress responses. The functional analysis of these modules showed enrichment of pathways important for adaptation of radiation or desiccation stress. To decipher the regulatory roles of these stress responsive modules, we identified transcription factors (TFs) and then calculated a Biweight mid correlation between modules hub gene and the identified TFs. We obtained 7 TFs for radiation and desiccation responsive modules. The expressions of 3 TFs were validated in response to gamma radiation using qRT-PCR. Along with the TFs, selected close neighbor genes of two important TFs, viz., DR_0997 (CRP) and DR_2287 (AsnC family transcriptional regulator) in the darkgreen module were also validated. In our network, among 13 hub genes associated with 13 modules, the functionality of 5 hub genes which are annotated as hypothetical proteins (hypothetical hub genes) in D. radiodurans genome has been revealed. Overall the study provided a better insight of pathways and regulators associated with relevant DNA damaging stress response in D. radiodurans.


Assuntos
Adaptação Fisiológica/genética , Deinococcus/genética , Deinococcus/fisiologia , Redes Reguladoras de Genes , Estresse Fisiológico , Biologia de Sistemas , Análise de Sequência com Séries de Oligonucleotídeos , Reprodutibilidade dos Testes
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