RESUMO

Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease (Uncinaria sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes. We evaluated the association of host genetic diversity, body condition and immune response with hookworm resistance and/or clearance in the South American fur seal (Arctocephalus australis). Uninfected pups had higher heterozygosity than parasitized individuals, indicating a negative relationship between heterozygosity and the chances of infection. Likewise, pups that died of hookworm infection had lower heterozygosity than those that died of non-infectious causes. Interestingly, once infected, pups that survived hookworm infection had heterozygosities similar to pups that died of hookworm disease. However, pups that cleared the infection had a higher body mass and parasite-specific immunoglobulin G levels than those that did not recover or died of hookworm disease. Thus, although heterozygosity predicted resistance to and mortality from hookworm infections, it did not affect parasite clearance, which was facilitated by better body condition and adaptive immune responses. This demonstrates that host genetic variability and host-environment interactions influence disease dynamics, acting at different, well-defined stages of infection.

Assuntos

Otárias , Variação Genética , Infecções por Uncinaria , Animais , Otárias/parasitologia , Otárias/genética , Infecções por Uncinaria/veterinária , Infecções por Uncinaria/imunologia , Infecções por Uncinaria/parasitologia , Resistência à Doença/genética , Interações Hospedeiro-Parasita/genética , Ancylostomatoidea/genética , Feminino , Masculino

RESUMO

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.

RESUMO

BACKGROUND: Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir's genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. RESULTS: Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. CONCLUSIONS: Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.

Assuntos

Pseudotsuga , Pseudotsuga/genética , Adaptação Fisiológica/genética , Variação Genética/genética , Hibridização Genética , Seleção Genética , México , Polimorfismo de Nucleotídeo Único , Colúmbia Britânica

RESUMO

BACKGROUND: Zoonotic sporotrichosis caused by Sporothrix brasiliensis has become the main subcutaneous mycosis in Brazil. Minas Gerais (MG) is located in southeast Brazil and since 2015 has experienced an epidemic of zoonotic sporotrichosis. OBJECTIVES: This study aimed to reconstruct the epidemiological scenario of sporotrichosis from S. brasiliensis in recent epizooty in the Metropolitan Region of Belo Horizonte (MRBH), MG. METHODS: A total of 95 Sporothrix spp. isolates (Sporothirx brasiliensis n = 74, S. schenckii n = 11 and S. globosa n = 10) were subjected to Amplified Fragment Length Polymorphism (AFLP) genotyping and mating-type analysis to determine genetic diversity and population structure. Of these, 46 S. brasiliensis isolates were recovered from animals (cats n = 41 and dogs n = 5) from MRBH. RESULTS: Our study describes the high interspecific differentiation power of AFLP-based genotyping between the main phylogenetic Sporothrix groups. S. brasiliensis presents high genetic variability and pronounced population structure with geographically focused outbreaks in Brazil. The genetic groups include older genotypes from the prolonged epidemic in Southeast (Rio de Janeiro and São Paulo), South (Rio Grande do Sul), Northeast (Pernambuco) and new genotypes from the MRBH. Furthermore, we provide evidence of heterothallism mating strategy in pathogenic Sporothrix species. Genotypes originating in Rio de Janeiro and Pernambuco carry the predominant MAT1-2 idiomorph as opposed to genotypes from Rio Grande do Sul, which have the MAT1-1 idiomorph. We observed an overwhelming occurrence of MAT1-1 among MRBH isolates. CONCLUSION: Our study provides clear evidence of the predominance of a genetic group profile circulating in animals in Minas Gerais, independent of that disseminated from Rio de Janeiro. Our data can help us understand the genetic population processes that drive the evolution of this fungus in Minas Gerais and contribute to future mitigation actions for this ongoing epidemic.

Assuntos

Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Doenças do Gato , Epidemias , Variação Genética , Genótipo , Sporothrix , Esporotricose , Esporotricose/epidemiologia , Esporotricose/microbiologia , Brasil/epidemiologia , Sporothrix/genética , Sporothrix/classificação , Sporothrix/isolamento & purificação , Animais , Gatos , Cães , Doenças do Gato/microbiologia , Doenças do Gato/epidemiologia , Zoonoses/epidemiologia , Zoonoses/microbiologia , Filogenia , Doenças do Cão/epidemiologia , Doenças do Cão/microbiologia , Humanos

RESUMO

Maize (Zea mays ssp. mays) diverged from one of its wild relatives, the teosinte Zea mays ssp. parviglumis, in the lowlands of southwest Mexico approximately 9000 years ago. Following this divergence, maize rapidly expanded throughout the Americas, becoming a staple food. This dispersal was accompanied by significant demographic and selective changes, leading to the development of numerous local varieties with a complex evolutionary history that remains incompletely understood. In recent years, genomic advances have challenged traditional models of maize domestication and spread to South America. At least three distinct genetic lineages associated with different migratory waves have been described: ancestral Andean, ancestral Lowland, and Pan-American. Additionally, the significant role of the teosinte Zea mays ssp. mexicana, in the evolution of modern maize has been recently uncovered. Genomic studies have shed light into highland adaptation processes, revealing largely independent adaptation events in Meso- and South America. As new evidence emerges, the regional complexity underlying maize diversity and the need for comprehensive, multi-scale approaches become evident. In the face of climate change and evolving agricultural landscapes, the conservation of native maize in South America is of growing interest, with genomics serving as an invaluable tool for identifying and preserving the genetic variability of locally adapted germplasm.

RESUMO

Soybeans (Glycine max L.), originating in China, were introduced to South America in the late 19th century after passing through North America. South America is now a major soybean-producing region, accounting for approximately 40% of the global soybean production. Crops like soybeans gradually adapt to the local climate and human-selected conditions, resulting in beneficial variations during cultivation in different regions. Comparing the phenotypic and genetic variations in soybeans across different regions is crucial to determining the variations that may enhance soybean productivity. This study identified seed-related traits and conducted a genetic diversity analysis using 46 breeding soybean varieties from China and Uruguay. Compared to the Chinese soybean germplasm, the Uruguayan equivalent had a lower 100-grain weight, higher oil content, lower protein content, and higher soluble sugar content. Using ZDX1 gene chips, genetic typing was performed on the 46 breeding varieties. Cluster analysis based on SNP sites revealed significant differences in the genetic basis of Sino-Uruguayan soybean germplasm. Selection analysis, including nucleotide polymorphism (π) and fixation indexes (Fst), identified several genomic regions under selection between Sino-Uruguayan soybean germplasm. The selected intervals significantly enriched gene ontology (GO) terms related to protein metabolism. Additionally, differentiation occurred in genes associated with the oil content, seed weight, and cyst nematodes between Sino-Uruguayan soybean germplasm, such as GmbZIP123 and GmSSS1. These findings highlight the differences in seed-related phenotypes between Sino-Uruguay soybean germplasm and provide genomic-level insights into the mechanisms behind phenotypic differences, offering valuable references for understanding soybean evolution and molecular breeding.

RESUMO

Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015-2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.

Assuntos

Carya , Variação Genética , Fenótipo , Carya/genética , Carya/crescimento & desenvolvimento , Filogenia , Genótipo , México , Polimorfismo de Nucleotídeo Único , Análise de Componente Principal , Genética Populacional

RESUMO

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (H e = 0.55) was lower than reported in the mainland (H e = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad-Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna.

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Cedrela odorata es considerada la segunda especie más invasora de árboles en las Islas Galápagos. Esta especie está catalogada en el Apéndice II de CITES y sus poblaciones se encuentran amenazadas en Ecuador continental, pero paradójicamente en Galápagos es una especie de preocupación por su potencial invasor. Estudios genéticos pueden ayudar a entender la historia de invasión de especies introducidas que causan efectos en ecosistemas únicos como Galápagos. En este estudio, analizamos 9 marcadores microsatélites en individuos de Galápagos y Ecuador continental para describir la diversidad genética y estructura poblacional de C. odorata en Galápagos y explorar el origen e historia de invasión de esta especie. La diversidad genética encontrada para C. odorata en Galápagos (H e = 0.55) fue menor que la reportada en continente (H e = 0.81), pero mayor que la de otras especies de plantas insulares invasoras, lo que podría sugerir múltiples introducciones de esta especie a Galápagos. Nuestros resultados sugieren que la costa norte ecuatoriana es el origen más probable de C. odorata en Galápagos, aunque más estudios, como secuenciación del genoma completo, Rad­Seq y/o análisis de SNPs, son necesarios para confirmar este hecho. Además, de acuerdo con los escenarios propuestos, es posible que C. odorata haya sido introducida primero a San Cristóbal y/o Santa Cruz desde Ecuador continental. Después de estas introducciones iniciales, parece haber llegado a Isabela y Floreana desde San Cristóbal o Santa Cruz. Este es el primer estudio genético de C. odorata en Galápagos y el primer intento de esclarecer la historia de invasión de esta especie. La información obtenida en esta investigación podría apoyar estrategias de manejo para disminuir el impacto que C. odorata tiene sobre la flora y fauna nativa de estas islas.

RESUMO

BACKGROUND: A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data. RESULTS: The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds. CONCLUSIONS: The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Assuntos

Heterozigoto , Polimorfismo de Nucleotídeo Único , Sequenciamento Completo do Genoma , Animais , Bovinos/genética , Sequenciamento Completo do Genoma/métodos , Análise de Sequência com Séries de Oligonucleotídeos , Genoma , Genômica/métodos

RESUMO

Hard-to-reach communities represent Peru's main challenge for malaria elimination, but information about transmission in these areas is scarce. Here, we assessed Plasmodium vivax (Pv) and P. falciparum (Pf) transmission dynamics, resistance markers, and Pf hrp2/3 deletions in Nueva Jerusalén (NJ), a remote, indigenous community in the Peruvian Amazon with high population mobility. We collected samples from November 2019 to May 2020 by active (ACD) and passive case detection (PCD) in NJ. Parasites were identified with microscopy and PCR. Then, we analyzed a representative set of positive-PCR samples (Pv = 68, Pf = 58) using highly-multiplexed deep sequencing assays (AmpliSeq) and compared NJ parasites with ones from other remote Peruvian areas using population genetics indexes. The ACD intervention did not reduce malaria cases in the short term, and persistent malaria transmission was observed (at least one Pv infection was detected in 96% of the study days). In Nueva Jerusalen, the Pv population had modest genetic diversity (He = 0.27). Pf population had lower diversity (He = 0.08) and presented temporal clustering, one of these clusters linked to an outbreak in February 2020. Moreover, Pv and Pf parasites from NJ exhibited variable levels of differentiation (Pv Fst = 0.07-0.52 and Pf Fst = 0.11-0.58) with parasites from other remote areas. No artemisin resistance mutations but chloroquine (57%) and sulfadoxine-pyrimethamine (35-67%) were detected in NJ's Pf parasites. Moreover, pfhrp2/3 gene deletions were common (32-50% of parasites with one or both genes deleted). The persistent Pv transmission and the detection of a Pf outbreak with parasites genetically distinct from the local ones highlight the need for tailored interventions focusing on mobility patterns and imported infections in remote areas to eliminate malaria in the Peruvian Amazon.

Assuntos

Malária Falciparum , Malária Vivax , Plasmodium falciparum , Plasmodium vivax , Proteínas de Protozoários , Peru/epidemiologia , Humanos , Plasmodium falciparum/genética , Plasmodium falciparum/isolamento & purificação , Plasmodium vivax/genética , Plasmodium vivax/isolamento & purificação , Malária Falciparum/epidemiologia , Malária Falciparum/parasitologia , Malária Falciparum/transmissão , Malária Vivax/epidemiologia , Malária Vivax/parasitologia , Malária Vivax/transmissão , Proteínas de Protozoários/genética , Feminino , Masculino , Criança , Adulto , Antimaláricos/uso terapêutico , Antimaláricos/farmacologia , Adolescente , Resistência a Medicamentos/genética , Pessoa de Meia-Idade , Povos Indígenas/genética , Adulto Jovem , Pré-Escolar , Genômica/métodos , Variação Genética , Antígenos de Protozoários/genética

RESUMO

Mining is a major economic activity in many developing countries. However, it disturbs the environment, producing enormous quantities of waste, known as mine tailings, which can have deleterious environmental impact, due to their high heavy metals (HM) content. Often, foundation species that establish on mine tailings are good candidates to study the effects of HM bioaccumulation at different levels of biological organization. Prosopis laevigata is considered a HM hyperaccumulator which presents attributes of a foundation species (FS) and establishes naturally on mine tailings. We evaluated the bioaccumulation of Cu, Pb, and Zn in P. laevigata foliar tissue, the leaf micro- and macro-morphological characters, DNA damage, and population genetic effects. In total, 80 P. laevigata individuals (20/site) belonging to four populations: The individuals from both sites (exposed and reference) bioaccumulated HMs (Pb > Cu > Zn). However, in the exposed individuals, Pb and Cu bioaccumulation was significantly higher. Also, a significant effect of macro- and micro-morphological characters was registered, showing significantly lower values in individuals from the exposed sites. In addition, we found significant differences in genotoxic damage in P. laevigata individuals, between the exposed and reference sites. In contrast, for the micro-morphological characters, none of the analyzed metals had any influence. P. laevigata did not show significant differences in the genetic structure and diversity between exposed and reference populations. However, four haplotypes and four private alleles were found in the exposed populations. Since P. laevigata is a species that establishes naturally in polluted sites and bioaccumulates HM in its foliar tissues, the resulting genetic, individual and population effects have not been severe enough to show detrimental effects; hence, P. laevigata can be a useful tool in phytoremediation strategies for soils polluted with Pb and Cu, maintaining its important ecological functions.

Assuntos

Bioacumulação , Metais Pesados , Prosopis , Poluentes do Solo , Metais Pesados/metabolismo , Prosopis/metabolismo , Poluentes do Solo/metabolismo , Biomarcadores/metabolismo , Mineração , Monitoramento Ambiental/métodos

RESUMO

The greater muscle fiber cross-sectional area (CSA) is associated with greater skeletal muscle mass and strength, whereas muscle fiber atrophy is considered a major feature of sarcopenia. Muscle fiber size is a polygenic trait influenced by both environmental and genetic factors. However, the genetic variants underlying inter-individual differences in muscle fiber size remain largely unknown. The aim of our study was to determine whether 1535 genetic variants previously identified in a genome-wide association study of appendicular lean mass are associated with the CSA of fast-twitch muscle fibers (which better predict muscle strength) in the m. vastus lateralis of 148 physically active individuals (19 power-trained and 28 endurance-trained females, age 28.0 ± 1.1; 28 power-trained and 73 endurance-trained males, age 31.1 ± 0.8). Fifty-seven single-nucleotide polymorphisms (SNPs) were identified as having an association with muscle fiber size (p < 0.05). Of these 57 SNPs, 31 variants were also associated with handgrip strength in the UK Biobank cohort (n = 359,729). Furthermore, using East Asian and East European athletic (n = 731) and non-athletic (n = 515) cohorts, we identified 16 SNPs associated with athlete statuses (sprinter, wrestler, strength, and speed-strength athlete) and weightlifting performance. All SNPs had the same direction of association, i.e., the lean mass-increasing allele was positively associated with the CSA of muscle fibers, handgrip strength, weightlifting performance, and power athlete status. In conclusion, we identified 57 genetic variants associated with both appendicular lean mass and fast-twitch muscle fiber size of m. vastus lateralis that may, in part, contribute to a greater predisposition to power sports.

Assuntos

Fibras Musculares Esqueléticas , Polimorfismo de Nucleotídeo Único , Humanos , Masculino , Feminino , Polimorfismo de Nucleotídeo Único/genética , Adulto , Fibras Musculares Esqueléticas/patologia , Estudo de Associação Genômica Ampla , Genômica , Força da Mão , Força Muscular/genética , Atletas

RESUMO

The rubber tree, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg., is the sole plant worldwide utilized for the commercial production of natural rubber. Following years of breeding, there exists a wide array of germplasm differentiation in rubber trees. The exploration of diversity and population structure within rubber tree germplasm resources, alongside the establishment of core germplasm resources, is instrumental in elucidating the genetic background and facilitating the effective utilization and management of these resources. By employing SNP molecular marker technology, 195 rubber tree resources were amplified, their genetic diversity analyzed, and a fingerprint map was subsequently constructed. Through this process, the cold-resistant core germplasm of rubber trees was identified. The results revealed that the PIC, He, and pi values ranged from 0.0905 to 0.3750, 0.095 to 0.5000, and 0.0953 to 0.5013, respectively. Both group structure analysis and cluster analysis delineated the accessions into two groups, signifying a simple group structure. A core germplasm bank was established with a sampling ratio of 10%, comprising 21 accessions divided into two populations. Population G1 consists of 20 accessions, while population G2 comprises 1 accession. The research findings have led to the creation of a molecular database that is anticipated to contribute to the management and subsequent breeding applications of rubber tree accessions.

Assuntos

Variação Genética , Hevea , Polimorfismo de Nucleotídeo Único , Banco de Sementes , Hevea/genética , Temperatura Baixa , Filogenia

RESUMO

Bovine torovirus (BToV) is an enteric pathogen that may cause diarrhea in calves and adult cattle, which could result in economic losses due to weight loss and decreased milk production. This study aimed to report the presence, the genetic characterization and the evolution of BToV in calves in Uruguay. BToV was detected in 7.9% (22/278) of fecal samples, being identified in dairy (9.2%, 22/239) but not beef (0.0%, 0/39) calves. BToV was detected in both diarrheic (14%, 6/43) and non-diarrheic (13.2%, 5/38) dairy calves. In addition, BToV was detected in the intestinal contents of 14.9% (7/47) of naturally deceased dairy calves. A complete genome (28,446 nucleotides) was obtained, which was the second outside Asia and the first in Latin America. In addition, partial S gene sequences were obtained to perform evolutionary analyses. Nucleotide and amino acid substitutions within and between outbreaks/farms were observed, alerting the continuous evolution of the virus. Through Bayesian analysis using BEAST, a recent origin (mid-60s) of BToV, possibly in Asia, was estimated, with two introductions into Uruguay from Asia and Europe in 2004 and 2013, respectively. The estimated evolutionary rate was 1.80 × 10-3 substitutions/site/year. Our findings emphasize the importance of continued surveillance and genetic characterization for the effective management and understanding of BToV's global epidemiology and evolution.

Assuntos

Doenças dos Bovinos , Fezes , Genoma Viral , Filogenia , Infecções por Torovirus , Torovirus , Animais , Uruguai/epidemiologia , Bovinos , Torovirus/genética , Torovirus/isolamento & purificação , Torovirus/classificação , Fezes/virologia , Doenças dos Bovinos/virologia , Doenças dos Bovinos/epidemiologia , Infecções por Torovirus/veterinária , Infecções por Torovirus/virologia , Infecções por Torovirus/epidemiologia , Diarreia/virologia , Diarreia/veterinária , Diarreia/epidemiologia , Evolução Molecular

RESUMO

The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.

RESUMO

Background: Molecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil. Methods: This was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira-Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%. Results: Of a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C. Conclusion: Our findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.

Assuntos

Infecções por HIV , HIV-1 , Filogenia , Humanos , Brasil/epidemiologia , HIV-1/genética , HIV-1/classificação , Masculino , Estudos Transversais , Infecções por HIV/epidemiologia , Infecções por HIV/transmissão , Adulto , Feminino , Pessoa de Meia-Idade , Epidemiologia Molecular , Análise por Conglomerados , Adulto Jovem , Adolescente , Farmacorresistência Viral/genética

RESUMO

Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly, the phylogenetic analysis of the BZLF1 indicated two main clades with high support, BZ-A and BZ-B (PP > 0.85). Thus, the BZ-A clade was the most diverse clade associated with the main polymorphisms investigated, including the haplotype Type 1 + V3 (p < 0.001). Furthermore, the multigene phylogenetic analysis (MLA) between BZLF1 and the oncogene LMP1 showed specific clusters, revealing haplotypic segregation that previous single-gene phylogenies from both genes failed to demonstrate. Surprisingly, the LMP1 Raji-related variant clusters were shown to be more diverse, associated with BZ-A/B and the Type 2/1 + V3 haplotypes. Finally, due to the high haplotypic diversity of the Raji-related variants, the number of DNA recombination-inducing motifs (DRIMs) was evaluated within the different clusters defined by the MLA. Similarly, the haplotype BZ-A + Raji was shown to harbor a greater number of DRIMs (p < 0.001). These results call attention to the high haplotype diversity of EBV in southeast Brazil and strengthen the hypothesis of the recombinant potential of South American Raji-related variants via the LMP1 oncogene.

Assuntos

Infecções por Vírus Epstein-Barr , Variação Genética , Herpesvirus Humano 4 , Filogenia , Recombinação Genética , Herpesvirus Humano 4/genética , Humanos , Brasil , Infecções por Vírus Epstein-Barr/virologia , Infecções por Vírus Epstein-Barr/genética , Transativadores/genética , Masculino , Feminino , Haplótipos/genética , Adulto , Proteínas da Matriz Viral/genética , Criança , Pessoa de Meia-Idade , Adolescente , Latência Viral/genética , Pré-Escolar , Adulto Jovem

RESUMO

In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.

Assuntos

Evolução Molecular , Variação Genética , Filogenia , Infecções por Rotavirus , Rotavirus , Rotavirus/genética , Rotavirus/classificação , Brasil , Humanos , Infecções por Rotavirus/virologia , Genótipo , Animais

RESUMO

There has been very limited investigation regarding the genetic diversity of Mycobacterium tuberculosis (MTb) strains isolated from human immunodeficiency virus (HIV)-infected patients in Mexico. In this study, we isolated 93 MTb strains from pulmonary and extrapulmonary samples of HIV-infected patients treated in a public hospital in Mexico City to evaluate the genetic diversity using spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) typing (based on 24 loci). The cohort comprised 80 male and 13 female individuals. There was a positive correlation between a high HIV viral load (>100,000 copies) and extrapulmonary tuberculosis (TB) (r = 0.306, p = 0.008). Lineage 4 was the most frequent lineage (79 strains). In this lineage, we found the H clade (n = 24), including the Haarlem, H3, and H1 families; the T clade (n = 22), including T1 and T2; the X clade (n = 15), including X1 and X3; the LAM clade (n = 14), including LAM1, LAM2, LAM3, LAM6, and LAM9; the S clade (n = 2); Uganda (n = 1); and Ghana (n = 1). We also found 12 strains in the EAI clade belonging to lineage 1, including the EAI2-Manila and EAI5 families. Interestingly, we identified one strain belonging to the Beijing family, which is part of lineage 2. One strain could not be identified. This study reports high genetic diversity among MTb strains, highlighting the need for a molecular epidemiological surveillance system that can help to monitor the spread of these strains, leading to more appropriate measures for TB control in HIV-infected patients.