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1.
BMC Evol Biol ; 20(1): 118, 2020 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-32928096

RESUMO

BACKGROUND: The Chinese Isoetes L. are distributed in a stairway pattern: diploids in the high altitude and polyploids in the low altitude. The allopolyploid I. sinensis and its diploid parents I. yunguiensis and I. taiwanensis is an ideal system with which to investigate the relationships between polyploid speciation and the ecological niches preferences. RESULTS: There were two major clades in the nuclear phylogenetic tree, all of the populations of polyploid were simultaneously located in both clades. The chloroplast phylogenetic tree included two clades with different populations of the polyploid clustered with the diploids separately: I. yunguiensis with partial populations of the I. sinensis and I. taiwanensis with the rest populations of the I. sinensis. The crow node of the I. sinensis allopolyploid system was 4.43 Ma (95% HPD: 2.77-6.97 Ma). The divergence time between I. sinensis and I. taiwanensis was estimated to 0.65 Ma (95% HPD: 0.26-1.91 Ma). The narrower niche breadth in I.sinensis than those of its diploid progenitors and less niche overlap in the pairwise comparisons between the polyploid and its progenitors. CONCLUSIONS: Our results elucidate that I. yunguinensis and I. taiwanensis contribute to the speciation of I. sinensis, the diploid parents are the female parents of different populations. The change of altitude might have played an important role in allopolyploid speciation and the pattern of distribution of I. sinensis. Additionally, niche novelty of the allopolyploid population of I. sinensis has been detected, in accordance with the hypothesis that niche shift between the polyploids and its diploid progenitors is important for the establishment and persistence of the polyploids.


Assuntos
Adaptação Biológica , Diploide , Especiação Genética , Poliploidia , Traqueófitas/classificação , China , Ecossistema , Filogenia
2.
Proc Natl Acad Sci U S A ; 117(38): 23807-23814, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32873642

RESUMO

Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed "genetic tuning," actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection.


Assuntos
Adaptação Biológica/genética , Substituição de Aminoácidos/genética , Subtipo H7N9 do Vírus da Influenza A/genética , Subtipo H7N9 do Vírus da Influenza A/patogenicidade , Influenza Humana/virologia , RNA Replicase/genética , Proteínas Virais/genética , Sequenciamento de Nucleotídeos em Larga Escala , Interações Hospedeiro-Patógeno , Humanos , RNA Viral/genética , Análise de Sequência de RNA , Replicação Viral/genética
3.
J Pharmacol Sci ; 144(3): 129-138, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32921394

RESUMO

The traditional Japanese (Kampo) medicines yokukansan (YKS) and yokukansankachimpihange (YKSCH) have similar formulas and the same indications. In animals or cultured cells, the neuropharmacological actions of YKS are sometimes more beneficial than those of YKSCH. Since both drugs are used to treat sleep disorders in Japan, we examined the ameliorative effects of YKS and YKSCH on circadian rhythm disturbance and compared their efficacy using a mouse model of circadian rhythm disruption. Ramelteon was used as the positive control. Ramelteon treatment significantly reversed decreased running wheel activity during the advanced dark phase, indicating facilitation of circadian adaptation. YKS treatment also reversed the activity in the early period of drug treatment; however, it was not statistically significant. YKSCH treatment significantly reversed the decreased activity during the advanced dark phase. Plasma melatonin (MT) levels were significantly increased in the YKSCH but not in the YKS group. The ameliorative effect of YKSCH on rhythm disruption was significantly inhibited by coadministration of the MT2 receptor antagonist. Therefore, the therapeutic effect of YKSCH on circadian rhythm disruption would be attributable, to elevated endogenous MT levels. Taken together, YKS and YKSCH have different pharmacological properties and may be more precisely prescribed depending on patients' psychological symptoms.


Assuntos
Adaptação Biológica/efeitos dos fármacos , Ritmo Circadiano/efeitos dos fármacos , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/uso terapêutico , Medicina Kampo , Melatonina/metabolismo , Fitoterapia , Transtornos do Sono-Vigília/tratamento farmacológico , Animais , Masculino , Melatonina/sangue , Camundongos Endogâmicos C3H , Transtornos do Sono-Vigília/etiologia , Transtornos do Sono-Vigília/fisiopatologia
4.
PLoS Biol ; 18(9): e3000636, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32991578

RESUMO

The Myriapoda, composed of millipedes and centipedes, is a fascinating but poorly understood branch of life, including species with a highly unusual body plan and a range of unique adaptations to their environment. Here, we sequenced and assembled 2 chromosomal-level genomes of the millipedes Helicorthomorpha holstii (assembly size = 182 Mb; shortest scaffold/contig length needed to cover 50% of the genome [N50] = 18.11 Mb mainly on 8 pseudomolecules) and Trigoniulus corallinus (assembly size = 449 Mb, N50 = 26.78 Mb mainly on 17 pseudomolecules). Unique genomic features, patterns of gene regulation, and defence systems in millipedes, not observed in other arthropods, are revealed. Both repeat content and intron size are major contributors to the observed differences in millipede genome size. Tight Hox and the first loose ecdysozoan ParaHox homeobox clusters are identified, and a myriapod-specific genomic rearrangement including Hox3 is also observed. The Argonaute (AGO) proteins for loading small RNAs are duplicated in both millipedes, but unlike in insects, an AGO duplicate has become a pseudogene. Evidence of post-transcriptional modification in small RNAs-including species-specific microRNA arm switching-providing differential gene regulation is also obtained. Millipedes possesses a unique ozadene defensive gland unlike the venomous forcipules found in centipedes. We identify sets of genes associated with the ozadene that play roles in chemical defence as well as antimicrobial activity. Macro-synteny analyses revealed highly conserved genomic blocks between the 2 millipedes and deuterostomes. Collectively, our analyses of millipede genomes reveal that a series of unique adaptations have occurred in this major lineage of arthropod diversity. The 2 high-quality millipede genomes provided here shed new light on the conserved and lineage-specific features of millipedes and centipedes. These findings demonstrate the importance of the consideration of both centipede and millipede genomes-and in particular the reconstruction of the myriapod ancestral situation-for future research to improve understanding of arthropod evolution, and animal evolutionary genomics more widely.


Assuntos
Adaptação Biológica/genética , Artrópodes , Evolução Molecular , Genoma/genética , Animais , Artrópodes/classificação , Artrópodes/genética , Sequência de Bases , Elementos de DNA Transponíveis/genética , Genes Homeobox , Genoma de Inseto , Insetos/classificação , Insetos/genética , MicroRNAs/genética , Filogenia , Sintenia
5.
Biomed Res Int ; 2020: 9089768, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32923488

RESUMO

Purpose: We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods: Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results: Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion: Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.


Assuntos
Adaptação Biológica/genética , Coronavirus Felino/genética , Peritonite Infecciosa Felina/virologia , Panleucopenia Felina/virologia , Genoma Viral/genética , Animais , Teorema de Bayes , Gatos , China , Coronavirus Felino/fisiologia , Evolução Molecular , Fezes/virologia , Peritonite Infecciosa Felina/patologia , Panleucopenia Felina/patologia , Mutação , Filogenia , Recombinação Genética , Seleção Genética , Proteínas Virais/genética
6.
Ecotoxicol Environ Saf ; 203: 110961, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32888621

RESUMO

Cadmium (Cd), which seriously affects plant growth and crop production, is harmful to humans. Previous studies revealed ryegrass (Lolium multiflorum Lam.) exhibits Cd tolerance, and may be useful as a potential hyperaccumulator because of its wide distribution. In this study, the physiological and transcriptional responses of two ryegrass cultivars [i.e., high (LmHC) and low (LmLC) Cd tolerance] to Cd stress were investigated and compared. The Cd tolerance of LmHC was greater than that of LmLC at various Cd concentrations. The uptake of Evans blue dye revealed that Cd-induced root cell mortality was higher in LmLC than in LmHC after a 12-h Cd treatment. Furthermore, the content and influx rate of Cd in LmLC roots were greater than in LmHC roots under Cd stress conditions. The RNA sequencing and quantitative real-time PCR data indicated that the Cd transport regulatory genes (ABCG37, ABCB4, NRAMP4, and HMA5) were differentially expressed between the LmLC and LmHC roots. This expression-level diversity may contribute to the differences in the Cd accumulation and translocation between LmLC and LmHC. These findings may help clarify the physiological and molecular mechanisms underlying ryegrass responses to Cd toxicity. Additionally, ryegrass may be able to hyperaccumulate toxic heavy metals during the phytoremediation of contaminated soil.


Assuntos
Adaptação Biológica , Cádmio/metabolismo , Lolium/efeitos dos fármacos , Raízes de Plantas/efeitos dos fármacos , Poluentes do Solo/metabolismo , Transcrição Genética/efeitos dos fármacos , Adaptação Biológica/efeitos dos fármacos , Adaptação Biológica/genética , Biodegradação Ambiental , Cádmio/análise , Cádmio/toxicidade , Genes de Plantas , Lolium/química , Lolium/genética , Raízes de Plantas/química , Raízes de Plantas/genética , Poluentes do Solo/análise , Poluentes do Solo/toxicidade
7.
Ecotoxicol Environ Saf ; 203: 111037, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-32888596

RESUMO

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.


Assuntos
Adaptação Biológica/genética , Antibacterianos/toxicidade , Resistência Microbiana a Medicamentos/genética , Poluentes Ambientais/toxicidade , Genes Bacterianos/efeitos dos fármacos , Camada de Gelo/microbiologia , Metais Pesados/toxicidade , Adaptação Biológica/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/genética , Camada de Gelo/química , Índia , Metagenômica , Siquim
8.
Proc Natl Acad Sci U S A ; 117(34): 20672-20680, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32817464

RESUMO

Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data (e.g., evolve-and-resequence studies). These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one time point to be predictive of the changes at later time points, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time points and across replicates. We estimate that at least 17 to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances, we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.


Assuntos
Adaptação Biológica/genética , Frequência do Gene/genética , Seleção Genética/genética , Aclimatação/genética , Adaptação Fisiológica/genética , Alelos , Animais , Evolução Biológica , Evolução Molecular , Frequência do Gene/fisiologia , Deriva Genética , Genética Populacional/métodos , Genômica/métodos , Humanos , Modelos Genéticos , Herança Multifatorial/genética , Densidade Demográfica
9.
Virus Res ; 288: 198113, 2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-32771430

RESUMO

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is recognized as one of the life-threatening viruses causing the most destructive pandemic in this century. The genesis of this virus is still unknown. To elucidate its molecular evolution and regulation of gene expression, the knowledge of codon usage is a pre-requisite. In this study, an attempt was made to document the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SARS-CoV-2 in human and dog. The SARS-CoV-2 genome showed relative abundance of A and U nucleotides and relative synonymous codon usage analysis revealed that the preferred synonymous codons mostly end with A/U. The analysis of ENc-GC3s, Neutrality and Parity rule 2 plots indicated that natural selection and other undefined factors dominate the overall codon usage bias in SARS-CoV-2 whereas the impact of mutation pressure is comparatively minor. The codon adaptation index and relative codon deoptimization index of SARS-CoV-2 deciphered that human is more favoured host for adaptation compared to dog. These results enhance our understanding of the factors involved in evolution of the novel human SARS-CoV-2 and its adaptability in dog.


Assuntos
Adaptação Biológica/genética , Betacoronavirus/genética , Uso do Códon , Infecções por Coronavirus/virologia , Doenças do Cão/virologia , Genoma Viral , Pneumonia Viral/virologia , Animais , Gatos , Bovinos , Quirópteros , Cães , Evolução Molecular , Cavalos , Especificidade de Hospedeiro , Humanos , Mutação , Pandemias , Seleção Genética , Suínos
10.
BMC Evol Biol ; 20(1): 100, 2020 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-32778052

RESUMO

BACKGROUND: Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data. RESULTS: We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal. CONCLUSIONS: As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.


Assuntos
Alveolados/genética , Genética Populacional , Genômica , Adaptação Biológica , Animais , Recifes de Corais , Fluxo Gênico
11.
Curr Biol ; 30(15): R849-R857, 2020 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-32750338

RESUMO

There is no doubt that the novel coronavirus SARS-CoV-2 that causes COVID-19 is mutating and thus has the potential to adapt during the current pandemic. Whether this evolution will lead to changes in the transmission, the duration, or the severity of the disease is not clear. This has led to considerable scientific and media debate, from raising alarms about evolutionary change to dismissing it. Here we review what little is currently known about the evolution of SARS-CoV-2 and extend existing evolutionary theory to consider how selection might be acting upon the virus during the COVID-19 pandemic. Although there is currently no definitive evidence that SARS-CoV-2 is undergoing further adaptation, continued evidence-based analysis of evolutionary change is important so that public health measures can be adjusted in response to substantive changes in the infectivity or severity of COVID-19.


Assuntos
Betacoronavirus/fisiologia , Evolução Biológica , Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Adaptação Biológica/genética , Animais , Infecções Assintomáticas , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Infecções por Coronavirus/transmissão , Pleiotropia Genética , Variação Genética , Humanos , Mutação , Pandemias , Pneumonia Viral/transmissão , Crescimento Demográfico , Seleção Genética , Distância Social , Zoonoses
12.
Proc Natl Acad Sci U S A ; 117(36): 22484-22493, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32848072

RESUMO

The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohemorrhagic Escherichia coli (EHEC) to d-serine (d-Ser) resulted in down-regulation of type 3 secretion system-dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens, adaptive evolution. In this study, we have explored the adaptation of EHEC to d-Ser and its consequences for pathogenesis. We rapidly isolated multiple, independent, EHEC mutants whose growth was no longer compromised in the presence of d-Ser. Through a combination of whole-genome sequencing and transcriptomics, we showed that tolerance could be attributed to disruption of one of two d-Ser transporters and/or activation of a previously nonfunctional d-Ser deaminase. While the implication of cytoplasmic transport in d-Ser toxicity was unsurprising, disruption of a single transporter, CycA, was sufficient to completely overcome the repression of type 3 secretion system activity normally associated with exposure to d-Ser. Despite the fact that this reveals a mechanism by which evolution could drive a pathogen to colonize new niches, interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highlighting a strong selective pressure for functionality. Collectively, these data show that CycA is a critically important conduit for d-Ser uptake that is central to the niche restriction of EHEC.


Assuntos
Escherichia coli Êntero-Hemorrágica , Genoma Bacteriano , Serina/farmacologia , Adaptação Biológica/genética , Escherichia coli Êntero-Hemorrágica/efeitos dos fármacos , Escherichia coli Êntero-Hemorrágica/genética , Escherichia coli Êntero-Hemorrágica/metabolismo , Técnicas de Silenciamento de Genes , Genoma Bacteriano/efeitos dos fármacos , Genoma Bacteriano/genética , Células HeLa , Humanos , Mutação/genética , Sistemas de Secreção Tipo III/genética
13.
BMC Res Notes ; 13(1): 398, 2020 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-32854762

RESUMO

OBJECTIVE: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.


Assuntos
Betacoronavirus/genética , Coronaviridae/genética , Recombinação Genética , Glicoproteína da Espícula de Coronavírus/genética , Adaptação Biológica/genética , Animais , Sítios de Ligação/genética , Quirópteros/virologia , Eutérios/virologia , Evolução Molecular , Furina/metabolismo , Especificidade de Hospedeiro , Humanos , Peptidil Dipeptidase A/metabolismo , Filogenia , Seleção Genética , Glicoproteína da Espícula de Coronavírus/metabolismo
14.
PLoS One ; 15(8): e0238151, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32833990

RESUMO

Bacteria often possess relatively flexible genome structures and adaptive genetic variants that allow survival in unfavorable growth conditions. Bacterial survival tactics in disadvantageous microenvironments include mutations that are beneficial against threats in their niche. Here, we report that the aerobic rice bacterial pathogen Burkholderia glumae BGR1 changes a specific gene for improved survival in static culture conditions. Static culture triggered formation of colony variants with deletions or point mutations in the gene bspP (BGLU_RS28885), which putatively encodes a protein that contains PDC2, PAS-9, SpoIIE, and HATPase domains. The null mutant of bspP survived longer in static culture conditions and produced a higher level of bis-(3'-5')-cyclic dimeric guanosine monophosphate than the wild type. Expression of the bacterial cellulose synthase regulator (bcsB) gene was upregulated in the mutant, consistent with the observation that the mutant formed pellicles faster than the wild type. Mature pellicle formation was observed in the bspP mutant before pellicle formation in wild-type BGR1. However, the population density of the bspP null mutant decreased substantially when grown in Luria-Bertani medium with vigorous agitation due to failure of oxalate-mediated detoxification of the alkaline environment. The bspP null mutant was less virulent and exhibited less effective colonization of rice plants than the wild type. All phenotypes caused by mutations in bspP were recovered to those of the wild type by genetic complementation. Thus, although wild-type B. glumae BGR1 prolonged viability by spontaneous mutation under static culture conditions, such genetic changes negatively affected colonization in rice plants. These results suggest that adaptive gene sacrifice of B. glumae to survive unfavorable growth conditions is not always desirable as it can adversely affect adaptability in the host.


Assuntos
Adaptação Biológica/genética , Burkholderia/genética , Burkholderia/metabolismo , Burkholderia/patogenicidade , Regulação Bacteriana da Expressão Gênica/genética , Genoma Bacteriano/genética , Genômica/métodos , Mutação , Oryza/microbiologia , Doenças das Plantas/microbiologia , Percepção de Quorum/genética , Virulência/genética
15.
Science ; 369(6502): 460-466, 2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32703880

RESUMO

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here, we show that multiple linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema, we found that a megabase-size "supermutation" has deleted color loci in green morphs. Moreover, we found that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help to package gene complexes into discrete units of diversity such as morphs, ecotypes, or species.


Assuntos
Adaptação Biológica/genética , Mutação , Neópteros/fisiologia , Animais , Evolução Biológica , Pigmentação
16.
Proc Natl Acad Sci U S A ; 117(31): 18582-18590, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32680961

RESUMO

Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations of Escherichia coli with genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.


Assuntos
Adaptação Biológica/genética , Evolução Molecular , Modelos Genéticos , Seleção Genética/genética , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Mutação/genética , Fator Tu de Elongação de Peptídeos/genética , Biossíntese de Proteínas/genética
17.
J Gen Virol ; 101(9): 925-940, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32568027

RESUMO

The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of non-structural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (remdesivir, alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that - upon passaging in Vero E6 cells - SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays.


Assuntos
Betacoronavirus/fisiologia , Vírus da SARS/fisiologia , Replicação Viral/fisiologia , Adaptação Biológica , Animais , Anticorpos Antivirais/imunologia , Betacoronavirus/genética , Linhagem Celular/ultraestrutura , Linhagem Celular/virologia , Chlorocebus aethiops , Biologia Computacional , Sequência Conservada , Reações Cruzadas , Efeito Citopatogênico Viral , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Soros Imunes/imunologia , Cinética , Camundongos , Microscopia Eletrônica , Microscopia de Fluorescência , RNA Viral/isolamento & purificação , Coelhos , Células Vero/ultraestrutura , Células Vero/virologia
18.
Appl Environ Microbiol ; 86(17)2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32561582

RESUMO

The discovery of the novel Zetaproteobacteria class greatly expanded our understanding of neutrophilic, microaerophilic microbial Fe(II) oxidation in marine environments. Despite molecular techniques demonstrating their global distribution, relatively few isolates exist, especially from low-Fe(II) environments. Furthermore, the Fe(II) oxidation pathways used by Zetaproteobacteria remain poorly understood. Here, we present the genomes (>99% genome completeness) of two Zetaproteobacteria, which are the only cultivated isolates originating from typical low-Fe [porewater Fe(II), 70 to 100 µM] coastal marine sediments. The two strains share <90% average nucleotide identity (ANI) with each other and <80% ANI with any other Zetaproteobacteria genome. The closest relatives were Mariprofundus aestuarium strain CP-5 and Mariprofundus ferrinatatus strain CP-8 (96 to 98% 16S rRNA gene sequence similarity). Fe(II) oxidation of strains KV and NF is most likely mediated by the putative Fe(II) oxidase Cyc2. Interestingly, the genome of strain KV also encodes a putative multicopper oxidase, PcoAB, which could play a role in Fe(II) oxidation, a pathway found only in two other Zetaproteobacteria genomes (Ghiorsea bivora TAG-1 and SCGC AB-602-C20). The strains show potential adaptations to fluctuating O2 concentrations, indicated by the presence of both cbb 3- and aa 3-type cytochrome c oxidases, which are adapted to low and high O2 concentrations, respectively. This is further supported by the presence of several oxidative-stress-related genes. In summary, our results reveal the potential Fe(II) oxidation pathways employed by these two novel chemolithoautotrophic Fe(II)-oxidizing species and the lifestyle adaptations which enable the Zetaproteobacteria to survive in coastal environments with low Fe(II) and regular redox fluctuations.IMPORTANCE Until recently, the importance and relevance of Zetaproteobacteria were mainly thought to be restricted to high-Fe(II) environments, such as deep-sea hydrothermal vents. The two novel Mariprofundus isolates presented here originate from typical low-Fe(II) coastal marine sediments. As well as being low in Fe(II), these environments are often subjected to fluctuating O2 concentrations and regular mixing by wave action and bioturbation. The discovery of two novel isolates highlights the importance of these organisms in such environments, as Fe(II) oxidation has been shown to impact nutrients and trace metals. Genome analysis of these two strains further supported their lifestyle adaptation and therefore their potential preference for coastal marine sediments, as genes necessary for surviving dynamic O2 concentrations and oxidative stress were identified. Furthermore, our analyses also expand our understanding of the poorly understood Fe(II) oxidation pathways used by neutrophilic, microaerophilic Fe(II) oxidizers.


Assuntos
Adaptação Biológica , Compostos Ferrosos/metabolismo , Genoma Bacteriano , Sedimentos Geológicos/microbiologia , Proteobactérias/genética , Meio Ambiente , Oxirredução , Filogenia , Água do Mar/microbiologia
19.
Exp Parasitol ; 216: 107916, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32590020

RESUMO

Complex life cycle parasites can manipulate the behavior of intermediate hosts in order to reduce their fitness and increase the chance of completing life cycle. In order to understand the effects of the trematode parasites of the genus Clinostomum on host fish Loricariichthys platymetopon, a filmed experiment was carried out to quantify the foraging activity of hosts with different intensities of infection. The results suggest that hosts with higher parasite intensities reduced foraging activity early in the morning when compared to hosts with low intensities. This period may be critical for hosts since birds, the target hosts of such trematodes, forage intensively at dawn.


Assuntos
Peixes-Gato/fisiologia , Peixes-Gato/parasitologia , Doenças dos Peixes/parasitologia , Trematódeos/fisiologia , Infecções por Trematódeos/veterinária , Adaptação Biológica , Animais , Comportamento Animal , Evolução Biológica , Brasil , Comportamento Alimentar , Doenças dos Peixes/epidemiologia , Doenças dos Peixes/fisiopatologia , Interações Hospedeiro-Parasita , Prevalência , Rios , Infecções por Trematódeos/epidemiologia , Infecções por Trematódeos/parasitologia , Infecções por Trematódeos/fisiopatologia , Gravação em Vídeo
20.
Sci Data ; 7(1): 187, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561793

RESUMO

Tarim red deer (Cervus elaphus yarkandensis) is the only subspecies of red deer (of 22 subspecies) from Central Asia. This species is a desert dweller of the Tarim Basin of southern Xinjiang, China, and exhibits some unique adaptations to the dry and extreme hot climate. We report here the assembly of a Tarim red deer genome employing a 10X Genomics library, termed CEY_v1. Our genome consisted of 2.6 Gb with contig N50 and scaffold N50 of 275.5 Kb and 31.7 Mb, respectively. Around 96% of the assembled sequences were anchored onto 34 chromosomes based on the published high-quality red deer genetic linkage map. More than 94% BUSCOs complete genes (including 90.5% single and 3.6% duplicated ones) were detected in the CEY_v1 and 20,653 genes were annotated. The CEY_v1 is expected to contribute to comparative analysis of genome biology, to evolutionary studies within Cervidae, and to facilitating investigation of mechanisms underlying adaptation of this species to the extreme dry and hot climate.


Assuntos
Mapeamento Cromossômico , Cervos/genética , Genoma , Adaptação Biológica , Animais , China , Clima , Ligação Genética , Anotação de Sequência Molecular , Filogenia , Análise de Sequência de DNA
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