Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 6.057
Filtrar
1.
BMC Plant Biol ; 19(1): 367, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31429697

RESUMO

BACKGROUND: Adaptation to abiotic stresses is crucial for the survival of perennial plants in a natural environment. However, very little is known about the underlying mechanisms. Here, we adopted a liquid culture system to investigate plant adaptation to repeated salt stress in Populus trees. RESULTS: We first evaluated phenotypic responses and found that plants exhibit better stress tolerance after pre-treatment of salt stress. Time-course RNA sequencing (RNA-seq) was then performed to profile changes in gene expression over 12 h of salt treatments. Analysis of differentially expressed genes (DEGs) indicated that significant transcriptional reprogramming and adaptation to repeated salt treatment occurred. Clustering analysis identified two modules of co-expressed genes that were potentially critical for repeated salt stress adaptation, and one key module for salt stress response in general. Gene Ontology (GO) enrichment analysis identified pathways including hormone signaling, cell wall biosynthesis and modification, negative regulation of growth, and epigenetic regulation to be highly enriched in these gene modules. CONCLUSIONS: This study illustrates phenotypic and transcriptional adaptation of Populus trees to salt stress, revealing novel gene modules which are potentially critical for responding and adapting to salt stress.


Assuntos
Adaptação Fisiológica/genética , Regulação da Expressão Gênica de Plantas , Populus/genética , Estresse Salino/genética , Transcrição Genética , Ontologia Genética , Redes Reguladoras de Genes , Genoma de Planta , Fenótipo , Populus/fisiologia , RNA de Plantas , Análise de Sequência de RNA , Transcriptoma , Árvores/genética , Árvores/fisiologia
2.
BMC Evol Biol ; 19(1): 150, 2019 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-31340758

RESUMO

BACKGROUND: Understanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria. RESULTS: We set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes. CONCLUSION: Overall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging.


Assuntos
Adaptação Fisiológica/genética , Ciclídeos/genética , Comportamento Alimentar , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Variação Genética , Arcada Osseodentária/anatomia & histologia , Animais , Ecossistema , Redes Reguladoras de Genes , Lagos , Larva/genética , Morfogênese/genética , Faringe/metabolismo , Filogenia , Padrões de Referência , Tanzânia
3.
BMC Plant Biol ; 19(1): 267, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221078

RESUMO

BACKGROUND: Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes. RESULTS: Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame. CONCLUSION: The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.


Assuntos
Secas , Sesamum/genética , Adaptação Fisiológica/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genótipo , Metabolômica , Sesamum/fisiologia
4.
Arch Virol ; 164(7): 1771-1780, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31076910

RESUMO

A number of avian avulavirus 1 (AAvV 1) isolates have been reported from avian and non-avian hosts worldwide with varying clinical consequences. In this regard, robust surveillance coupled with advanced diagnostics, genomic analysis, and disease modelling has provided insight into the molecular epidemiology and evolution of this virus. The genomic and evolutionary characteristics of AAvV 1 isolates originating from avian hosts have been well studied, but those originating from non-avian hosts have not. Here, we report a comparative genomic and evolutionary analysis of so-far reported AAvV 1 isolates originating from hosts other than avian species (humans, mink and swine). Phylogenetic analysis showed that AAvV 1 isolates clustered in five distinct genotypes (I, II, VI, VII and XIII). Further analysis revealed clustering of isolates into clades distant enough to be considered distinct subgenotypes, along with a few substitutions in several significant motifs. Although further investigation is needed, the clustering of AAvV 1 strains isolated from non-avian hosts into novel subgenotypes and the presence of substitutions in important structural and biological motifs suggest that this virus can adapt to novel hosts and therefore could have zoonotic potential.


Assuntos
Adaptação Fisiológica/genética , Infecções por Avulavirus/epidemiologia , Avulavirus/genética , Avulavirus/isolamento & purificação , Doenças das Aves/virologia , Especificidade de Hospedeiro/genética , Sequência de Aminoácidos , Animais , Avulavirus/classificação , Genótipo , Humanos , Vison , Epidemiologia Molecular , Filogenia , Alinhamento de Sequência , Suínos
5.
Plant Biol (Stuttg) ; 21(5): 783-795, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31081234

RESUMO

Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.


Assuntos
Fagaceae/fisiologia , Adaptação Fisiológica/genética , Mudança Climática , Fagaceae/genética , Variação Genética , Estresse Fisiológico
6.
Sci Total Environ ; 681: 191-201, 2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31103657

RESUMO

Mangrove forests are an important contributor to the coastal marine environment. They have developed unique adaptations to the harsh coastal wetland, yet their geographic distribution is limited by environmental temperature. The adaptive strategies of mangrove at the molecular level, however, have not been addressed. In the present work, transcriptome analyses were performed on different cold damaged plants of a mangrove species, Kandelia obovata. From the samples collected in the field after a cold stress, we found that distinct expression profiles of many key genes are related to extreme temperature responses. These include transcription factors such as WRKY and bHLH, and other genes encoding proteins like SnRK2, PR-1, KCS, involving in the pathways of plant hormones, plant-pathogen interactions, and long chain fatty acid synthesis. We also examined the transcriptomes of eight tissues of K. obovata to identify candidate genes involved in adaptation and development. While stress-responsive genes were globally expressed, tissue-specific genes with diverse functions might be involved in tissue development and adaptability. For examples, genes encoding CYP724B1 and ABCB1 were specifically expressed in the fruit and root, respectively. Additionally, 26 genes were identified as positively selected genes in K. obovata, six of them were found to be involved in chilling stress response, seed germination and oxidation-reduction processes, suggesting their roles in stressful environment adaptation. Together, these results shed light into the K. obovata's natural responses to cold snaps at the molecular level, and reveal a global gene expression portrait across different tissues. It also provides a transcriptome resource for further molecular ecology studies and conservation planning of this and other mangrove plants in their native and adopted environments.


Assuntos
Adaptação Fisiológica/genética , Rhizophoraceae/fisiologia , Temperatura Baixa , Perfilação da Expressão Gênica , Reguladores de Crescimento de Planta , Rhizophoraceae/genética , Transcriptoma , Áreas Alagadas
7.
BMC Evol Biol ; 19(1): 99, 2019 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-31068148

RESUMO

BACKGROUND: RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show gene duplication and loss-most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of antiviral RNAi in insects, but has repeatedly formed new testis-specific duplicates in the recent history of the obscura species-group of Drosophila. RESULTS: Here we take advantage of publicly available genomic and transcriptomic data to identify six further RNAi-pathway genes that have duplicated in this clade of Drosophila, and examine their evolutionary history. As seen for Ago2, we observe high levels of adaptive amino-acid substitution and changes in sex-biased expression in many of the paralogs. However, our phylogenetic analysis suggests that co-duplications of the RNAi machinery were not synchronous, and our expression analysis fails to identify consistent male-specific expression. CONCLUSIONS: These results confirm that RNAi genes, including genes of the antiviral and piRNA pathways, have undergone multiple independent duplications and that their history has been particularly labile within the obscura group. However, they also suggest that the selective pressures driving these changes have not been consistent, implying that more than one selective agent may be responsible.


Assuntos
Adaptação Fisiológica/genética , Drosophila/genética , Duplicação Gênica , Genes de Insetos , Interferência de RNA , Substituição de Aminoácidos/genética , Animais , Teorema de Bayes , Proteínas CLOCK/genética , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Evolução Molecular , Regulação da Expressão Gênica , Masculino , Filogenia
8.
BMC Plant Biol ; 19(1): 218, 2019 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-31133003

RESUMO

BACKGROUND: An eukaryotic translation elongation factor-2 (eEF-2) plays an important role in protein synthesis, however, investigation on its role in abiotic stress responses is limited. A cold responsive eEF2 named as MfEF2 was isolated from yellow-flowered alfalfa [Medicago sativa subsp. falcata (L.) Arcang, thereafter M. falcata], a forage legume with great cold tolerance, and transgenic tobacco (Nicotiana tabacum L.) plants overexpressing MfEF2 were analyzed in cold tolerance and proteomic profiling was conducted under low temperature in this study. RESULTS: MfEF2 transcript was induced and peaked at 24 h and remained at the high level during cold treatment up to 96 h. Overexpression of MfEF2 in trasngenic tobacco plants resulted in enhanced cold tolerance. Compared to the wild type, transgenic plants showed higher survival rate after freezing treatment, higher levels of net photosynthetic rate (A), maximum photochemical efciency of photosystem (PS) II (Fv/Fm) and nonphotochemical quenching (NPQ) and lower levels of ion leakage and reactive oxygen species (ROS) production after chilling treatment. iTRAQ-based quantitative proteomic analysis identified 336 differentially expressed proteins (DEPs) from leaves of one transgenic line versus the wild type after chilling treatment for 48 h. GO and KEGG enrichment were conducted for analysis of the major biological process, cellular component, molecular function, and pathways of the DEPs involving in. It is interesting that many down-regulated DEPs were grouped into "photosynthesis" and "photosynthesis-antenna", such as subunits of PSI and PSII as well as light harvesting chlorophyll protein complex (LHC), while many up-regulated DEPs were grouped into "spliceosome". CONCLUSIONS: The results suggest that MfEF2 confers cold tolerance through regulating hundreds of proteins synthesis under low temperature conditions. The elevated cold tolerance in MfEF2 transgenic plants was associated with downregulation of the subunits of PSI and PSII as well as LHC, which leads to reduced capacity for capturing sunlight and ROS production for protection of plants, and upregulation of proteins involving in splicesome, which promotes alternative splicing of pre-mRNA under low temperature.


Assuntos
Adaptação Fisiológica/genética , Regulação da Expressão Gênica de Plantas , Medicago/fisiologia , Fator 2 de Elongação de Peptídeos/genética , Proteínas de Plantas/genética , Tabaco/fisiologia , Temperatura Baixa , Medicago/genética , Fator 2 de Elongação de Peptídeos/metabolismo , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/fisiologia , Estresse Fisiológico/genética , Tabaco/genética
9.
Vet Res ; 50(1): 26, 2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30992061

RESUMO

Thioredoxins (Trxs) play an important role in defending against oxidative stress and keeping disulfide bonding correct to maintain protein function. Edwardsiella piscicida, a severe fish pathogen, has been shown to encode several thioredoxins including TrxA, TrxC, and TrxH, but their biological roles remain unknown. In this study, we characterized TrxH of E. piscicida (named TrxHEp) and examined its expression and function. TrxHEp is composed of 125 residues and possesses typical thioredoxin H motifs. Expression of trxHEp was upregulated under conditions of oxidative stress, iron starvation, low pH, and during infection of host cells. trxHEp expression was also regulated by ferric uptake regulator (Fur), an important global regulatory of E. piscicida. Compared to the wild type TX01, a markerless trxHEp in-frame mutant strain TX01∆trxH exhibited markedly compromised tolerance of the pathogen to hydrogen peroxide, acid stress, and iron deficiency. Deletion of trxHEp significantly retarded bacterial biofilm growth and decreased resistance against serum killing. Pathogenicity analysis shows that the inactivation of trxHEp significantly impaired the ability of E. piscicida to invade host cells, reproduce in macrophages, and infect host tissues. Introduction of a trans-expressed trxH gene restored the lost virulence of TX01∆trxH. There is likely to be a complex relationship of functional complementation or expression regulation between TrxH and another two thioredoxins, TrxA and TrxC, of E. piscicida. This is the first functional report of TrxH in fish pathogens, and the findings suggest that TrxHEp is essential for coping with adverse circumstances and contributes to host infection of E. piscicida.


Assuntos
Proteínas de Bactérias/genética , Edwardsiella/fisiologia , Edwardsiella/patogenicidade , Regulação Bacteriana da Expressão Gênica , Tiorredoxina h/genética , Transcriptoma , Adaptação Fisiológica/genética , Sequência de Aminoácidos , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Edwardsiella/genética , Alinhamento de Sequência , Tiorredoxina h/química , Tiorredoxina h/metabolismo , Virulência
10.
Vet Microbiol ; 232: 151-155, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31030840

RESUMO

Influenza virus-like sequences of H17N10 and H18N11 were identified in bats, despite there has been no live virus isolated. The genetic analysis indicated that they have distinct but relatively close evolutionary relationships to known influenza A viruses. However, the infectivity and adaptation of bat influenza viruses in avian species remain unclear. In this study, two modified bat influenza viruses cH9cN2/H17 and cH9cN2/H18 containing HA and NA coding regions replaced with those of H9N2 influenza A virus were generated in the background of the H17N10 or H18N11 viruses. These two modified viruses replicated less efficiently than wild type H9N2 virus in cultured chicken cells. The mini-genome assay showed that viral ribonucleoproteins (vRNPs) of H9N2 has significantly higher polymerase activity than that of bat influenza viruses in avian cells. In chicken study, compared with H9N2 virus, which replicated and transmitted efficiently in chickens, the cH9cN2/H17 and cH9cN2/H18 viruses only replicated in chicken tracheas with lower titers. Pathological examination showed that the H9N2 caused severer lesions in lung and trachea than the modified bat influenza viruses. Notably, the cH9cN2/H18 transmitted among chickens, but not cH9cN2/H17, and chicken IFN-ß antagonism results showed that H18N11 NS1 protein inhibited chicken IFN-ß response more efficiently than H17N10 NS1 protein in avian cells. Taken together, our data indicated that the internal genes of bat influenza viruses adapted poorly to chickens, while the internal genes of H18N11 seemed to adapt to chickens better than H17N10.


Assuntos
Adaptação Fisiológica/genética , Quimera/genética , Quirópteros/virologia , Vírus da Influenza A Subtipo H9N2/genética , Orthomyxoviridae/genética , Animais , Sequência de Bases , Galinhas/virologia , Hemaglutininas Virais/genética , Influenza Aviária/virologia , Neuraminidase/genética , Doenças das Aves Domésticas/virologia , Ribonucleoproteínas
11.
Phys Rev E ; 99(2-1): 022139, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30934317

RESUMO

Elements of statistical physics formalism were applied to mutagenic and carcinogenic processes associated with cellular DNA; these are lesion (damage) creation, mutation creation, and cellular neoplastic (cancer) transformation. The probabilities of all state changes were strictly related to potential barrier heights between energetic states of DNA molecules. Barriers can be modified when radiation adaptive response mechanisms are applied, which are associated with a radiobiological quantity called radiosensitivity. It was discussed that radiosensitivity is determined by the cell's response to radiation resulting in three potential dose-response scenarios: linear, threshold, or hormetic. The type of dose-response is of critical importance in the development of radiation protection standards and individual radiation risk assessment. It is shown that the different scenarios describe different limits of the same underlying phenomena and the cell can respond in a linear, threshold, or hormetic way regarding its radiosensitivity. Finally, the dissipative adaptation mechanism is discussed in the context of proliferating cancer cells.


Assuntos
Adaptação Fisiológica/efeitos da radiação , Neoplasias/fisiopatologia , Estatística como Assunto , Adaptação Fisiológica/genética , Transformação Celular Neoplásica/genética , Transformação Celular Neoplásica/efeitos da radiação , Dano ao DNA , Modelos Biológicos , Mutação/efeitos da radiação , Neoplasias/genética , Neoplasias/patologia , Tolerância a Radiação/genética
12.
Plant Sci ; 282: 40-48, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31003610

RESUMO

Improved genetic, genomic and statistical technologies have increased the capacity to enrich breeding populations for key alleles underpinning adaptation and continued genetic gain. In turn, directed genomic selection together with increased heritability will reduce genetic variance to narrow the genetic base in many crop breeding programs. Diverse genetic resources (GR), including wild and weedy relatives, landraces and reconstituted synthetics, have potential to contribute novel alleles for key traits. Targeted trait identification may also identify genetic diversity in addressing new challenges including the need for modified root architecture, greater nutrient-use efficiency, and adaptation to warmer air and soil temperatures forecast with climate change. Yet while core collections and other GR sources have historically been invaluable for major gene control of disease and subsoil constraints, the mining of genetically (and phenotypically) complex traits in GR remains a significant challenge owing to reduced fertility, limited seed quantities and poor adaptation through linkage drag with undesirable alleles. High-throughput field phenomics (HTFP) offers the opportunity to capture phenotypically complex variation underpinning adaptation in traditional phenotypic selection or statistics-based breeding programs. Targeted HTFP will permit the reliable phenotyping of greater numbers of GR-derived breeding lines using smaller plot sizes and at earlier stages of population development to reduce the duration of breeding cycles and the loss of potentially important alleles with linkage drag. Two key opportunities are highlighted for use of HTFP in selection among GR-derived wheat breeding lines for greater biomass and stomatal conductance through canopy temperature.


Assuntos
Melhoramento Vegetal , Adaptação Fisiológica/genética , Adaptação Fisiológica/fisiologia , Mudança Climática , Variação Genética/genética , Genômica , Fenótipo
13.
Nat Plants ; 5(4): 369-379, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30962527

RESUMO

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.


Assuntos
Domesticação , Sorghum/genética , Adaptação Fisiológica/genética , Produtos Agrícolas/genética , Produtos Agrícolas/história , História Antiga , Hibridização Genética/genética , Característica Quantitativa Herdável
14.
BMC Genomics ; 20(1): 283, 2019 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-30975079

RESUMO

BACKGROUND: Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis. RESULTS: A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis. CONCLUSIONS: This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis. Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.


Assuntos
Bacillus/genética , Evolução Molecular , Genômica , Adaptação Fisiológica/genética , Bacillus/metabolismo , Bacillus/fisiologia , Família Multigênica/genética , Filogenia
15.
Int J Mol Sci ; 20(8)2019 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-31010109

RESUMO

Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous-Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, Ceratopteris thalictroides, for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site (Ks) between paralogs; Ks age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a Ks peak value of approximately 1.2 was obtained for both samples; however, the Ks frequency distributions varied significantly. Importantly, we dated the WGD event at 51-53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as C. thalictroides, which exhibits higher temperature tolerance.


Assuntos
Adaptação Fisiológica/genética , Gleiquênias/genética , Duplicação Gênica , Genes Duplicados , Genoma de Planta , Cromossomos de Plantas/genética , Diploide , Genes de Plantas , Proteínas de Domínio MADS/genética , Modelos Genéticos , Família Multigênica , Filogenia , Poliploidia
16.
Food Microbiol ; 82: 426-435, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31027802

RESUMO

Salmonella enterica serotypes have been reported as the agent of various outbreaks occurred after the consumption of low water activity (aw) foods. When the pathogen encounters harsh conditions, several regulatory networks are activated through dynamic differential gene expression that lead to cell survival for prolonged periods. In this work, the transcriptome of S. enterica serovar Typhimurium using RNA-Seq, after cells' inoculation in four distinct types of low aw foods (milk chocolate, powdered milk, black pepper, and dried pet food), following storage at 25 °C per 24 and 72 h was studied. The findings of this study suggest that gene regulation is influenced by the food composition mainly in the first 24 h post-inoculum, proceeded by the induction of similar genes shared among all samples. It was possible to evaluate the differences on each type of food matrix regarding the bacteria adaptation, as well as the similarities provoked by low aw. The results reveal genes that may play key roles in response to desiccation in Salmonella, as well as the pathways in which they are involved.


Assuntos
Adaptação Fisiológica/genética , Proteínas de Bactérias/genética , Microbiologia de Alimentos , Salmonella typhimurium/genética , Água/análise , Proteínas de Bactérias/metabolismo , Análise por Conglomerados , Dessecação , Análise de Alimentos , Perfilação da Expressão Gênica , Regulação Bacteriana da Expressão Gênica , Salmonella typhimurium/fisiologia
17.
BMC Evol Biol ; 19(1): 89, 2019 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-30975078

RESUMO

BACKGROUND: Standard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that provide protection from predators. We performed a survey and identified at least two species with a lifespan of over 20 years. Given their small size and ease of captive reproduction, clownfish lend themselves as experimental models of exceptional longevity. To identify genetic correlates of exceptional longevity, we sequenced the transcriptomes of Amphiprion percula and A. clarkii and performed a scan for positively-selected genes (PSGs). RESULTS: The PSGs that we identified in the last common clownfish ancestor were compared with PSGs detected in long-lived mole rats and short-lived killifishes revealing convergent evolution in processes such as mitochondrial biogenesis. Among individual genes, the Mitochondrial Transcription Termination Factor 1 (MTERF1), was positively-selected in all three clades, whereas the Glutathione S-Transferase Kappa 1 (GSTK1) was under positive selection in two independent clades. For the latter, homology modelling strongly suggested that positive selection targeted enzymatically important residues. CONCLUSIONS: These results indicate that specific pathways were recruited in independent lineages evolving an exceptionally extended or shortened lifespan and point to mito-nuclear balance as a key factor.


Assuntos
Evolução Biológica , Longevidade/genética , Fases de Leitura Aberta/genética , Perciformes/genética , Adaptação Fisiológica/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Éxons/genética , Proteínas de Peixes/química , Proteínas de Peixes/genética , Ontologia Genética , Biogênese de Organelas , Filogenia
18.
Pak J Biol Sci ; 22(2): 95-102, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30972991

RESUMO

BACKGROUND AND OBJECTIVE: The partial-submergence-tolerant crop plants, including rice are required for fulfilling food needs when a flooding disaster occurs in Indonesia. The information of effective selection method for obtaining submergence tolerant rice is required for increasing the North Sulawesi capacity as a pillar of national food security. This study evaluated the partial-submergence-tolerance in 10 rice cultivars that are cultivated in North Sulawesi Province based on the morphological characters (plant height, shoot dry mass, shoot length, root dry mass, root length, root volume, shoot:root ratio and leaf number) at the vegetative phase. MATERIAL AND METHODS: This experiment was conducted in the greenhouse using 10 rice cultivars (cv. Cigeulis, Seruni, Mekongga, Ciherang, TB, Ombong, Inpari 13, Burungan, Temo and Superwin). These cultivars were grown at the vegetative phase in partial submergence condition (the entire root system and 30 cm of above-ground shoot was under water) for 20 days, with 8 replicates, in a randomized block design. RESULTS: The longer duration of partial-submergence treatment resulted in the decrease of leaf number, the increase of plant height and the increase of shoot elongation. There were three categories of partial-submergence tolerance, i.e., tolerant for Cigeulis and TB, semi tolerant for Seruni, Mekongga, Inpari 13, Burungan, Temo and Superwin and non-tolerant for Ciherang and Ombong. CONCLUSION: Rice cv. TB as tolerant cultivar showed better growth response under partial submergence rather than other rice cultivars at the vegetative phase.


Assuntos
Adaptação Fisiológica/genética , Adaptação Fisiológica/fisiologia , Oryza/crescimento & desenvolvimento , Oryza/fisiologia , Inundações , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Indonésia , Oryza/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/fisiologia , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/fisiologia
19.
Food Microbiol ; 82: 316-324, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31027789

RESUMO

Biofilm-forming Bacillus species are often involved in contamination of dairy products and therefore present a major microbiological challenge in the field of food quality and safety. In this study, we sequenced and analyzed the genomes of milk- and non-milk-derived Bacillus strains, and evaluated their biofilm-formation potential in milk. Unlike non-dairy Bacillus isolates, the dairy-associated Bacillus strains were characterized by formation of robust submerged and air-liquid interface biofilm (pellicle) during growth in milk. Moreover, genome comparison analysis revealed notable differences in putative biofilm-associated determinants between the dairy and non-dairy Bacillus isolates, which correlated with biofilm phenotype. These results suggest that biofilm formation by Bacillus species might represent a presumable adaptation strategy to the dairy environment.


Assuntos
Adaptação Fisiológica , Bacillus/fisiologia , Biofilmes/crescimento & desenvolvimento , Leite/microbiologia , Adaptação Fisiológica/genética , Animais , Bacillus/classificação , Bacillus/genética , Bacillus/crescimento & desenvolvimento , Análise por Conglomerados , DNA Bacteriano/genética , Microbiologia de Alimentos , Genes Bacterianos/genética , Variação Genética , Genoma Bacteriano/genética , Análise de Sequência de DNA
20.
J Basic Microbiol ; 59(7): 680-691, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30997929

RESUMO

Although arsenic (As) is recognized as a toxic element for living species, some microorganisms have the ability to tolerate and transform it; recent studies have proposed to take advantage of such capacity to develop sustainable bioremediation strategies. In this study, we evaluated the adaptation to increasing concentrations of As(III) and As(V) of three metabolically different microbial cultures (heterotrophic, autotrophic-acidophilic, and anaerobic) obtained from a sample with low-soluble As content from the Copahue geothermal system. At the end of the adaptation process, the heterotrophic culture was able to grow at 20 mM and 450 mM of As(III) and As(V), respectively; the autotrophic-acidophilic culture showed tolerance to 15 mM of As(III) and 150 mM of As(V), whereas the anaerobic culture only developed in As(V) at concentrations up to 50 mM. The most tolerant consortia were characterized by their growth performance, complexity, and the presence of genes related to As metabolism and resistance. Regarding the consortia complexity, the predominant genera identified were: Paenibacillus in both heterotrophic consortia, Acidithiobacillus in the autotrophic-acidophilic consortium tolerant to As(III), Acidiphilium in the autotrophic-acidophilic consortium tolerant to As(V), and Thiomonas and Clostridium in the anaerobic consortium. This study is the first report of As tolerance microorganisms obtained from Copahue and reasserts the versatility and flexibility of the community of this natural extreme environment; also, it opens the door to the study of possible uses of these consortia in the design of biotechnological processes where the As concentration may fluctuate.


Assuntos
Adaptação Fisiológica/fisiologia , Arsênico/metabolismo , Bactérias/metabolismo , Biodegradação Ambiental , Sedimentos Geológicos/microbiologia , Fontes Termais/microbiologia , Consórcios Microbianos/fisiologia , Adaptação Fisiológica/genética , Anaerobiose , Argentina , Arsênico/química , Processos Autotróficos , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodiversidade , Meios de Cultura/química , Sedimentos Geológicos/química , Processos Heterotróficos , Fontes Termais/química , Consórcios Microbianos/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA