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1.
Gene ; 764: 145090, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-32861880

RESUMO

Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world. The species often suffers from cold stress. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two contrasting cultivars of L. vannamei, namely, cold-tolerant Guihai 2 (GH2) and cold-sensitive Guihai1 (GH1), under a control temperature (28 °C), cold stress (16 °C), and recovery to 28 °C. A total of 84.5 Gb of sequences were generated from 12 L. vannamei hepatopancreas libraries. The de-novo assembly generated a total of 143,029 unigenes with a mean size of 1,052 bp and an N50 of 2,604 bp, of which 34.08% were annotated in the Nr database. We analyzed the differentially expressed genes (DEGs) between nine comparison groups and detected a total of 21,026 DEGs. KEGG pathways, including lysosome, sphingolipid metabolism and nitrogen metabolism, were significantly enriched by DEGs between different temperatures in GH2. Furthermore, eight of the most significantly DEGs under cold stress from the transcriptomic analysis were selected for quantitative real-time PCR (qPCR) validation. Overall, we compared gene expression changes under cold stress in cold-tolerant and cold-sensitive L. vannamei for the first time. The results may further extend our understanding of the cold stress-response mechanism in L. vannamei.


Assuntos
Aclimatação/genética , Resposta ao Choque Frio/genética , Hepatopâncreas/metabolismo , Penaeidae/fisiologia , Frutos do Mar , Animais , Aquicultura , China , Temperatura Baixa/efeitos adversos , Regulação da Expressão Gênica/fisiologia , Anotação de Sequência Molecular , RNA-Seq , Reação em Cadeia da Polimerase em Tempo Real , Transcriptoma/genética
2.
Gene ; 764: 145097, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-32866589

RESUMO

Tomato (Lycopersicon esculentum Mill) is an important food plant that has been used as a model plant in genetic evolution and molecular biology research. The plant is originated from the tropics; thus, it is sensitive to cold. Its growth and development can be easily affected by cold stress. In this study, cold-regulated gene LeCOR413PM2 was cloned from tomato leaves and then used to generate two types of transgenic tomato plants: LeCOR413PM2-overexpressing transgenic plants and RNA-interference-expressing transgenic plants. The functions and expression of LeCOR413PM2 gene in response to cold stress were subsequently assessed. The results showed that LeCOR413PM2 localized in the plasma membrane. Expression of LeCOR413PM2 gene in the leaf of transgenic tomato plant was highest compared to that in other organs (i.e., root, stem, flower and fruit); it was elevated when plants were treated with cold stress. Overexpression of LeCOR413PM2 gene was found to not only reduce damage to cell membrane, accumulation of ROS, and photoinhibition of PSII, but also maintain high activity of antioxidant enzymes and content of osmotic regulators. The results also reveal that high activities of antioxidant enzymes were caused by the up-regulation of their gene expressions. This study demonstrates that the overexpression of LeCOR413PM2 could increase cold tolerance of transgenic tomato plants, while the suppressed expression of LeCOR413PM2 by RNA interference could increase the sensitivity of plants to cold.


Assuntos
Aclimatação/genética , Resposta ao Choque Frio/genética , Regulação da Expressão Gênica de Plantas , Lycopersicon esculentum/fisiologia , Proteínas de Plantas/genética , Membrana Celular/metabolismo , Clonagem Molecular , Temperatura Baixa/efeitos adversos , Genes de Plantas , Osmose/fisiologia , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Interferência de RNA , Espécies Reativas de Oxigênio/metabolismo
3.
PLoS Genet ; 16(11): e1009110, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33216740

RESUMO

Organisms living in seasonally variable environments utilize cues such as light and temperature to induce plastic responses, enabling them to exploit favorable seasons and avoid unfavorable ones. Local adapation can result in variation in seasonal responses, but the genetic basis and evolutionary history of this variation remains elusive. Many insects, including Drosophila melanogaster, are able to undergo an arrest of reproductive development (diapause) in response to unfavorable conditions. In D. melanogaster, the ability to diapause is more common in high latitude populations, where flies endure harsher winters, and in the spring, reflecting differential survivorship of overwintering populations. Using a novel hybrid swarm-based genome wide association study, we examined the genetic basis and evolutionary history of ovarian diapause. We exposed outbred females to different temperatures and day lengths, characterized ovarian development for over 2800 flies, and reconstructed their complete, phased genomes. We found that diapause, scored at two different developmental cutoffs, has modest heritability, and we identified hundreds of SNPs associated with each of the two phenotypes. Alleles associated with one of the diapause phenotypes tend to be more common at higher latitudes, but these alleles do not show predictable seasonal variation. The collective signal of many small-effect, clinally varying SNPs can plausibly explain latitudinal variation in diapause seen in North America. Alleles associated with diapause are segregating in Zambia, suggesting that variation in diapause relies on ancestral polymorphisms, and both pro- and anti-diapause alleles have experienced selection in North America. Finally, we utilized outdoor mesocosms to track diapause under natural conditions. We found that hybrid swarms reared outdoors evolved increased propensity for diapause in late fall, whereas indoor control populations experienced no such change. Our results indicate that diapause is a complex, quantitative trait with different evolutionary patterns across time and space.


Assuntos
Aclimatação/genética , Evolução Biológica , Diapausa de Inseto/genética , Drosophila melanogaster/fisiologia , Transcriptoma/fisiologia , Alelos , Altitude , Animais , Clima , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Genoma de Inseto/genética , Estudo de Associação Genômica Ampla , Herança Multifatorial , América do Norte , Locos de Características Quantitativas , Estações do Ano , Análise Espaço-Temporal , Zâmbia
4.
Sci Rep ; 10(1): 17203, 2020 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-33057204

RESUMO

Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.


Assuntos
Adaptação Fisiológica/genética , Fabaceae/genética , Redes Reguladoras de Genes/genética , MicroRNAs/genética , Aclimatação/genética , Secas , Regulação da Expressão Gênica de Plantas/genética , Estudo de Associação Genômica Ampla/métodos , Proteínas de Plantas/genética , Processamento Pós-Transcricional do RNA/genética , Estresse Fisiológico/genética , Transcriptoma/genética
5.
Proc Natl Acad Sci U S A ; 117(44): 27694-27702, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33077597

RESUMO

Abscisic acid (ABA) is the key phytohormone in plant drought tolerance and stress adaptation. The clade A protein phosphatase 2Cs (PP2Cs) like ABI1 (ABA-INSENSITIVE 1) work as coreceptors of ABA and regulate multiple ABA responses. Ubiquitination of ABI1 has been proven to play important regulatory roles in ABA signaling. However, the specific ubiquitin conjugating enzyme (E2) involved is unknown. Here, we report that UBC27 is an active E2 that positively regulates ABA signaling and drought tolerance. UBC27 forms the E2-E3 pair with the drought regulator RING E3 ligase AIRP3. Both UBC27 and AIRP3 interact with ABI1 and affect the ubiquitination and degradation of ABI1. ABA activates the expression of UBC27, inhibits the proteasome degradation of UBC27, and enhances the interaction between UBC27 and ABI1 to increase its activity. These findings uncover a regulatory mechanism in ABA signaling and drought response and provide a further understanding of the plant ubiquitination system and ABA signaling pathway.


Assuntos
Ácido Abscísico/metabolismo , Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiologia , Fosfoproteínas Fosfatases/metabolismo , Enzimas de Conjugação de Ubiquitina/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Aclimatação/genética , Proteínas de Arabidopsis/genética , Secas , Retroalimentação Fisiológica , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Mutação , Fosfoproteínas Fosfatases/genética , Plantas Geneticamente Modificadas , Proteólise , Transdução de Sinais/genética , Enzimas de Conjugação de Ubiquitina/genética , Ubiquitinação
6.
PLoS One ; 15(10): e0240435, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33044983

RESUMO

Acclimation to environmental changes driven by alterations in gene expression will serve as an important response for some species facing rapid Anthropogenic climate change. Pikas, genus Ochotona, are particularly vulnerable to climate change and current trends suggest that only the highest, coldest elevations within their ranges may remain suitable habitat for these species. In this study we aimed to assess the role of changes in gene expression in potentially facilitating elevational movements in pikas by measuring gene expression in the only known captive pika population, Ochotona dauurica, in response to hypoxic conditions. Using a controlled experiment, we exposed four male pikas to oxygen concentrations characteristic of sea-level, 2,000 m, and 4,000 m for 5 days each. Using blood samples collected after each treatment, we used RNAseq to determine if candidate pathways were undergoing significant changes in gene expression at different levels of oxygen (~100%, ~77%, and ~61% of sea-level oxygen concentrations). Gene set enrichment analyses showed that gene sets associated with the oxidative phosphorylation pathway and electron transport chain were significantly enriched for up-regulated genes in the 4,000 m samples compared to samples from the same individuals at lower-elevation conditions. Up-regulation of these pathways is consistent with known mechanisms of oxygen compensation. Our results suggest that these pikas have the acclimation capacity to tolerate oxygen concentrations characteristic of any elevation within their species range and that gene expression can be changed in a matter of days to accommodate drastically different oxygen concentrations. Thus, rapid and radical elevational movements that may be required of some pika species to avoid warmer temperatures in the Anthropocene will likely not be limited by hypoxic stress.


Assuntos
Aclimatação/genética , Mudança Climática , Ecossistema , Regulação da Expressão Gênica , Hipóxia/fisiopatologia , Lagomorpha , Oxigênio/metabolismo , Altitude , Animais , Perfilação da Expressão Gênica , Masculino , Temperatura
7.
Nat Commun ; 11(1): 5155, 2020 10 14.
Artigo em Inglês | MEDLINE | ID: mdl-33056995

RESUMO

The diverse physiological functions of tocotrienols have listed them as valuable supplementations to α-tocopherol-dominated Vitamin E products. To make tocotrienols more readily available, tocotrienols-producing S. cerevisiae has been constructed by combining the heterologous genes from photosynthetic organisms with the endogenous shikimate pathway and mevalonate pathway. After identification and elimination of metabolic bottlenecks and enhancement of precursors supply, the engineered yeast can produce tocotrienols at yield of up to 7.6 mg/g dry cell weight (DCW). In particular, proper truncation of the N-terminal transit peptide from the plant-sourced enzymes is crucial. To further solve the conflict between cell growth and tocotrienols accumulation so as to enable high-density fermentation, a cold-shock-triggered temperature control system is designed for efficient control of two-stage fermentation, leading to production of 320 mg/L tocotrienols. The success in high-density fermentation of tocotrienols by engineered yeast sheds light on the potential of fermentative production of vitamin E tocochromanols.


Assuntos
Fermentação/fisiologia , Microbiologia Industrial/métodos , Engenharia Metabólica , Saccharomyces cerevisiae/metabolismo , Tocotrienóis/metabolismo , Aclimatação/genética , Vias Biossintéticas/genética , Temperatura Baixa/efeitos adversos , Resposta ao Choque Frio/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Regulação Fúngica da Expressão Gênica , Mutação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
8.
Nat Commun ; 11(1): 4928, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004791

RESUMO

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.


Assuntos
Aclimatação/genética , Cromatina/metabolismo , Grupos Étnicos/genética , Redes Reguladoras de Genes , Modelos Genéticos , Altitude , Doença da Altitude/etnologia , Doença da Altitude/genética , Doença da Altitude/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Hipóxia Celular/genética , Células Cultivadas , Cromatina/genética , Sequenciamento de Cromatina por Imunoprecipitação , Resistência à Doença/genética , Feminino , Regulação da Expressão Gênica , Células Endoteliais da Veia Umbilical Humana , Humanos , Hipóxia/genética , Hipóxia/metabolismo , Oxigênio/metabolismo , Polimorfismo de Nucleotídeo Único , Gravidez , Cultura Primária de Células , RNA-Seq , Elementos Reguladores de Transcrição/genética , Seleção Genética , Tibet/etnologia , Fatores de Transcrição/metabolismo , Sequenciamento Completo do Genoma
9.
Nat Commun ; 11(1): 4897, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994415

RESUMO

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.


Assuntos
Carbono/análise , Metagenoma/genética , Microbiota/fisiologia , Microbiologia do Solo , Solo/química , Aclimatação/genética , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Carbono/metabolismo , Ciclo do Carbono , Celulose/metabolismo , DNA Ambiental/genética , DNA Ambiental/isolamento & purificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Aquecimento Global , Pradaria , Temperatura Alta/efeitos adversos , Metagenômica , Modelos Genéticos , Raízes de Plantas/química , Poaceae/química
10.
PLoS One ; 15(8): e0236186, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866164

RESUMO

AIM: To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes. METHODS AND FINDINGS: 42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT). CONCLUSIONS: Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.


Assuntos
Aclimatação/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes , Estresse Fisiológico/genética , Triticum/genética , China , Análise por Conglomerados , Conjuntos de Dados como Assunto , Secas , Perfilação da Expressão Gênica , Genes de Plantas , Melhoramento Vegetal/métodos , RNA-Seq , Seleção Genética
11.
Sci Rep ; 10(1): 14098, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32839518

RESUMO

The highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29-585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.


Assuntos
Aclimatação/genética , Organismos Aquáticos/genética , Meio Ambiente , Genoma/genética , Urocordados/genética , Urocordados/fisiologia , Animais , Organismos Aquáticos/fisiologia , Chile , Fluxo Gênico/genética , Frequência do Gene/genética , Genética Populacional , Genótipo , Oceano Pacífico , Filogeografia , Polimorfismo de Nucleotídeo Único/genética
12.
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
13.
PLoS One ; 15(8): e0237334, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32776991

RESUMO

We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.


Assuntos
Aclimatação/genética , Secas , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/genética , Oryza/fisiologia , Composição de Bases , Uso do Códon , Simulação por Computador , Perfilação da Expressão Gênica , Estudo de Associação Genômica Ampla
14.
Sci Rep ; 10(1): 11213, 2020 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-32641697

RESUMO

The Tibetan chicken is a unique breed that has adapted to the high-altitude hypoxic conditions of the Tibetan plateau. A number of positively selected genes have been reported in these chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. In the present study, eggs from Tibetan and Chahua chickens were incubated under hypoxic and normoxic conditions, and vascularization in the chorioallantoic membrane (CAM) of embryos was observed. We found that the vessel density index in the CAM of Tibetan chickens was lower than in Chahua chickens under hypoxia conditions. Transcriptomic and proteomic analyses of CAM tissues were performed in Tibetan and Chahua chicken embryos under hypoxic incubation using RNA-Seq and iTRAQ. We obtained 160 differentially expressed genes and 387 differentially expressed proteins that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaptation of chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.


Assuntos
Aclimatação/genética , Altitude , Galinhas/fisiologia , Hipóxia/fisiopatologia , Animais , Circulação Sanguínea/genética , Embrião de Galinha , Membrana Corioalantoide/irrigação sanguínea , Regulação da Expressão Gênica no Desenvolvimento , Neovascularização Fisiológica/genética , Proteoma/fisiologia , Proteômica , RNA-Seq , Tibet , Transcriptoma/fisiologia
15.
Nature ; 584(7822): 602-607, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32641831

RESUMO

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.


Assuntos
Ecótipo , Haplótipos , Helianthus/genética , Aclimatação/genética , Alelos , Flores/genética , Helianthus/anatomia & histologia , Helianthus/crescimento & desenvolvimento , Filogenia , Sementes/genética
16.
Arch Microbiol ; 202(10): 2841-2847, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32681430

RESUMO

Planococcus halotolerans, recently described as a novel species with SCU63T as the type strain, is capable of thriving in up to 15% NaCl and temperatures as low as 0 °C. To better understand its adaptation strategies at the genomic level, strain SCU63T was subjected to whole-genome sequencing and data mining. The high-quality assembly yielded 17 scaffolds with a genome size of 3,622,698 bp. Its genome harbors 3683 protein-coding sequences and 127 RNA genes, as well as three biosynthetic gene clusters and 25 genomic islands. The phylogenomic tree provided compelling insights into the evolutionary relationships of Planococcus. Comparative genomic analysis revealed key similarities and differences in the functional gene categories among Planococcus species. Strain SCU63T was shown to have diverse stress response systems for high salt and cold habitats. Further comparison with three related species showed the presence of numerous unique gene clusters in the SCU63T genome. The strain might serve as a good model for using extremozymes in various biotechnological processes.


Assuntos
Aclimatação/genética , Planococáceas/genética , Planococcus (Bactéria)/genética , Tolerância ao Sal/genética , Temperatura Baixa , Genômica , Família Multigênica/genética , Filogenia , Planococáceas/metabolismo , Planococcus (Bactéria)/metabolismo , Tolerância ao Sal/fisiologia , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
17.
High Alt Med Biol ; 21(3): 217-222, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32716669

RESUMO

Pun, Matiram, Rachel Turner, Giacomo Strapazzon, Hermann Brugger, and Erik R. Swenson. Lower incidence of COVID-19 at high altitude: Facts and confounders. High Alt Med Biol. 21:217-222, 2020.-The rapid transmission, increased morbidity, and mortality of coronavirus disease 2019 (COVID-19) has exhausted many health care systems and the global economy. Large variations in COVID-19 prevalence and incidence have been reported across and within many countries worldwide; however, this remains poorly understood. The variability and susceptibility across the world have been mainly attributed to differing socioeconomic status, burden of chronic diseases, access to health care, strength of health care systems, and early or late adoption of control measures. Environmental factors such as pollution, ambient temperature, humidity, and seasonal weather patterns at different latitudes may influence how severe the pandemic is and the incidence of infection in any part of the world. In addition, recent epidemiological data have been used to propose that altitude of residence may not only influence those environmental features considered key to lesser viral transmission, but also susceptibility to more severe forms of COVID-19 through hypoxic-hypobaria driven genomic or nongenomic adaptations specific to high-altitude populations. In this review, we critically examine these factors and attempt to determine based upon available scientific and epidemiological data whether living in high-altitude regions might be protective against COVID-19 as recent publications have claimed.


Assuntos
Altitude , Betacoronavirus , Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Aclimatação/genética , Infecções por Coronavirus/genética , Infecções por Coronavirus/virologia , Suscetibilidade a Doenças/virologia , Transmissão de Doença Infecciosa , Humanos , Incidência , Pandemias , Pneumonia Viral/genética , Pneumonia Viral/virologia
18.
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
19.
Sci Rep ; 10(1): 9081, 2020 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-32493917

RESUMO

Oceans are vast, dynamic, and complex ecosystems characterized by fluctuations in environmental parameters like sea surface temperature (SST), salinity, oxygen availability, and productivity. Environmental variability acts as the driver of organismal evolution and speciation as organisms strive to cope with the challenges. We investigated the evolutionary consequences of heterogeneous environmental conditions on the mitogenome of a widely distributed small pelagic fish of Indian ocean, Indian oil sardine, Sardinella longiceps. Sardines were collected from different eco-regions of the Indian Ocean and selection patterns analyzed in coding and non-coding regions. Signals of diversifying selection were observed in key functional regions involved in OXPHOS indicating OXPHOS gene regulation as the critical factor to meet enhanced energetic demands. A characteristic control region with 38-40 bp tandem repeat units under strong selective pressure as evidenced by sequence conservation and low free energy values was also observed. These changes were prevalent in fishes from the South Eastern Arabian Sea (SEAS) followed by the Northern Arabian Sea (NAS) and rare in Bay of Bengal (BoB) populations. Fishes belonging to SEAS exhibited accelerated substitution rate mainly due to the selective pressures to survive in a highly variable oceanic environment characterized by seasonal hypoxia, variable SST, and food availability.


Assuntos
Aclimatação/genética , Peixes/genética , Peixes/fisiologia , Genoma Mitocondrial/genética , Animais , Biomassa , Ecossistema , Oceano Índico , Salinidade , Temperatura
20.
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
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