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PURPOSE: Gallbladder cancer (GBC) is a biliary tract malignancy characterized by its high lethality. Although the incidence of GBC is low in most countries, specific areas such as Chile display a high incidence. Our collaborative study sought to compare clinical and molecular features of GBC cohorts from Chile and the United States with a focus on ERBB2 alterations. METHODS: Patients were accrued at Memorial Sloan Kettering Cancer Center (MSK) or the Pontificia Universidad Católica de Chile (PUC). Clinical information was retrieved from medical records. Genomic analysis was performed by the next-generation sequencing platform MSK-Integrated Mutation Profiling of Actionable Cancer Targets. RESULTS: A total of 260 patients with GBC were included, 237 from MSK and 23 from PUC. There were no significant differences in the clinical characteristics between the patients identified at MSK and at PUC except in terms of lithiasis prevalence which was significantly higher in the PUC cohort (85% v 44%; P = .0003). The prevalence of ERBB2 alterations was comparable between the two cohorts (15% v 9%; P = .42). Overall, ERBB2 alterations were present in 14% of patients (8% with ERBB2 amplification, 4% ERBB2 mutation, 1.5% concurrent amplification and mutation, and 0.4% ERBB2 fusion). Notably, patients with GBC that harbored ERBB2 alterations had better overall survival (OS) versus their ERBB2-wild type counterparts (22.3 months v 11.8 months; P = .024). CONCLUSION: The prevalence of lithiasis seems to be higher in Chilean versus US patients with GBC. A similar prevalence of ERBB2 alterations of overall 14% and better OS suggests that a proportion of them could benefit from human epidermal growth factor receptor type 2-targeted therapies. The smaller cohort of Chile, where the disease prevalence is higher, is a reminder and invitation for the need of more robust next-generation sequencing analyses globally.
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Neoplasias de la Vesícula Biliar , Receptor ErbB-2 , Humanos , Neoplasias de la Vesícula Biliar/genética , Neoplasias de la Vesícula Biliar/epidemiología , Neoplasias de la Vesícula Biliar/patología , Neoplasias de la Vesícula Biliar/mortalidad , Chile/epidemiología , Receptor ErbB-2/genética , Femenino , Masculino , Persona de Mediana Edad , Anciano , Estados Unidos/epidemiología , Mutación , Estudios de Cohortes , Adulto , Genómica , Anciano de 80 o más Años , Secuenciación de Nucleótidos de Alto RendimientoRESUMEN
Influenza circulation was significantly affected in 2020-21 by the COVID-19 pandemic. During this time, few influenza cases were recorded. However, in the summer of 2021-22, an increase in atypical influenza cases was observed, leading to the resurgence of influenza in the southernmost state of Brazil, Rio Grande do Sul (RS). The present study aimed to identify the circulation of FLUAV, FLUBV and SARS-CoV-2 and characterize the influenza genomes in respiratory samples using high-throughput sequencing technology (HTS). Respiratory samples (n = 694) from patients in RS were selected between July 2021 and August 2022. The samples were typed using reverse transcriptase real-time PCR (RT-qPCR) and showed 32% (223/694) of the samples to be positive for SARS-CoV-2, 7% for FLUAV (H3) (49/694). FLUBV was not detected. RT-qPCR data also resulted in FLUAV and SARS-CoV-2 co-infections in 1.7% (4/223) of samples tested. Whole genome sequencing of FLUAV produced 15 complete genomes of the H3N2 subtype, phylogenetically classified in the 3C.2a1b.2a.2a.3 subclade and revealing the dominance of viruses in the southern region of Brazil. Mutation analysis identified 72 amino acid substitutions in all genes, highlighting ongoing genetic evolution with potential implications for vaccine effectiveness, viral fitness, and pathogenicity. This study underscores limitations in current surveillance systems, advocating for comprehensive data inclusion to enhance understanding of influenza epidemiology in southern Brazil. These findings contribute valuable insights to inform more effective public health responses and underscore the critical need for continuous genomic surveillance.
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COVID-19 , Genoma Viral , Gripe Humana , Filogenia , SARS-CoV-2 , Humanos , Brasil/epidemiología , COVID-19/epidemiología , COVID-19/virología , SARS-CoV-2/genética , SARS-CoV-2/clasificación , SARS-CoV-2/aislamiento & purificación , Gripe Humana/epidemiología , Gripe Humana/virología , Persona de Mediana Edad , Adulto , Femenino , Genoma Viral/genética , Masculino , Adulto Joven , Anciano , Adolescente , Brotes de Enfermedades , Secuenciación Completa del Genoma , Niño , Preescolar , Lactante , Coinfección/epidemiología , Coinfección/virología , Secuenciación de Nucleótidos de Alto Rendimiento , Anciano de 80 o más Años , GenómicaRESUMEN
DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences.
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Elementos Transponibles de ADN , Genoma , Filogenia , Elementos Transponibles de ADN/genética , Animales , Genoma/genética , Evolución Molecular , Repeticiones de Microsatélite/genética , Genómica/métodos , Peces/genética , Peces/clasificaciónRESUMEN
BACKGROUND: Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1-2; 2-4 Mb FROH 2-4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). RESULTS: The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1-2, r = 0.20 with FROH 2-4 and r = 0.28 with FROH 4-8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH-genome (r = 0.60). The FROH-genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH-genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2-4 to 0.37 for FROH 1-2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19-0.59 for FGRM, 0.21-0.58 for FROH-genome, and 0.19-0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49-1.97% for FGRM, 0.34-2.2% for FROH-genome, and 0.50-1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. CONCLUSIONS: The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.
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Genómica , Depresión Endogámica , Endogamia , Linaje , Animales , Bovinos/genética , Genómica/métodos , Homocigoto , Femenino , Masculino , Polimorfismo de Nucleótido SimpleRESUMEN
This study aimed to evaluate the genomic profile of the Antarctic marine Curtobacterium sp. CBMAI 2942, as well as to optimize the conditions for chitinase production and antifungal potential for biological control. Assembly and annotation of the genome confirmed the genomic potential for chitinase synthesis, revealing two ChBDs of chitin binding (Chi C). The optimization enzyme production using an experimental design resulted in a 3.7-fold increase in chitinase production. The chitinase enzyme was identified by SDS-PAGE and confirmed through mass spectrometry analysis. The enzymatic extract obtained using acetone showed antifungal activity against the phytopathogenic fungus Aspergillus sp. series Nigri CBMAI 1846. The genetic capability of Curtobacterium sp. CBMAI 2942 for chitin degradation was confirmed through genomic analysis. The basal culture medium was adjusted, and the chitinase produced by this isolate from Antarctica showed significant inhibition against Aspergillus sp. Nigri series CBMAI 1846, which is a tomato phytopathogenic fungus. This suggests that this marine bacterium could potentially be used as a biological control of agricultural pests.
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Antifúngicos , Quitinasas , Proteómica , Quitinasas/metabolismo , Quitinasas/genética , Quitinasas/farmacología , Antifúngicos/farmacología , Regiones Antárticas , Proteómica/métodos , Genómica/métodos , Aspergillus/enzimología , Aspergillus/genética , Genoma Bacteriano , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Organismos Acuáticos , Quitina/farmacología , Quitina/metabolismo , Quitina/químicaRESUMEN
BACKGROUND: Helicobacter pylori infects the stomach and/or small intestines in more than half of the human population. Infection with H. pylori is the most common cause of chronic gastritis, which can lead to more severe gastroduodenal pathologies such as peptic ulcer, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. H. pylori infection is particularly concerning in Colombia in South America, where > 80% of the population is estimated to be infected with H. pylori and the rate of stomach cancer is one of the highest in the continent. RESULTS: We compared the antimicrobial susceptibility profiles and short-read genome sequences of five H. pylori isolates obtained from patients diagnosed with gastritis of varying severity (chronic gastritis, antral erosive gastritis, superficial gastritis) in Pereira, Colombia sampled in 2015. Antimicrobial susceptibility tests revealed the isolates to be resistant to at least one of the five antimicrobials tested: four isolates were resistant to metronidazole, two to clarithromycin, two to levofloxacin, and one to rifampin. All isolates were susceptible to tetracycline and amoxicillin. Comparative genome analyses revealed the presence of genes associated with efflux pump, restriction modification systems, phages and insertion sequences, and virulence genes including the cytotoxin genes cagA and vacA. The five genomes represent three novel sequence types. In the context of the Colombian and global populations, the five H. pylori isolates from Pereira were phylogenetically distant to each other but were closely related to other lineages circulating in the country. CONCLUSIONS: H. pylori from gastritis of different severity varied in their antimicrobial susceptibility profiles and genome content. This knowledge will be useful in implementing appropriate eradication treatment regimens for specific types of gastritis. Understanding the genetic and phenotypic heterogeneity in H. pylori across the geographical landscape is critical in informing health policies for effective disease prevention and management that is most effective at local and country-wide scales. This is especially important in Colombia and other South American countries that are poorly represented in global genomic surveillance studies of bacterial pathogens.
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Antibacterianos , Farmacorresistencia Bacteriana , Gastritis , Genoma Bacteriano , Infecciones por Helicobacter , Helicobacter pylori , Humanos , Helicobacter pylori/genética , Helicobacter pylori/efectos de los fármacos , Helicobacter pylori/patogenicidad , Helicobacter pylori/aislamiento & purificación , Gastritis/microbiología , Colombia , Infecciones por Helicobacter/microbiología , Antibacterianos/farmacología , Virulencia/genética , Farmacorresistencia Bacteriana/genética , Genómica , Pruebas de Sensibilidad Microbiana , Filogenia , Persona de Mediana Edad , Masculino , FemeninoRESUMEN
OBJECTIVES: The two oyster species studied hold considerable economic importance for artisanal harvest (Crassostrea rhizophorae) and aquaculture (Crassostrea gasar). Their draft genomes will play an important role in the application of genomic methods such as RNAseq, population-based genomic scans aiming at addressing expression responses to pollution stress, adaptation to salinity and temperature variation, and will also permit investigating the genetic bases and enable marker-assisted selection of economically important traits like shell and mantle coloration and resistance to temperature and disease. DATA DESCRIPTION: The draft assembly size of Crassostrea gasar is 506 Mbp, and of Crassostrea rhizophorae is 584 Mbp with scaffolds N50 of 11,3 Mbp and 4,9 Mbp, respectively. The general masked bases by RepeatMasker in both genomes were highly similar using different datasets. The masked bases varied from 9.41% in C. gasar to 10.05% in C. rhizophorae and 42.85% in C. gasar to 44.44% in C. rhizophorae using Dfam and RepeatModeler datasets, respectively. Functional annotation with eggNog resulted in 34,693 annotated proteins in C. rhizophorae and 26,328 in C. gasar. BUSCO analysis shows that almost 99% of genes (5,295) are complete in relation to the mollusk orthologous genes dataset (mollusca_odb10).
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Crassostrea , Genoma , Crassostrea/genética , Crassostrea/crecimiento & desarrollo , Animales , Genoma/genética , Acuicultura/métodos , Anotación de Secuencia Molecular , Genómica/métodos , Océano AtlánticoRESUMEN
Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava, a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species.
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Adaptación Fisiológica , Evolución Molecular , Gastrópodos , Polimorfismo de Nucleótido Simple , Animales , Gastrópodos/genética , Adaptación Fisiológica/genética , Genómica , Genotipo , GenomaRESUMEN
The relationships between plants and bacteria are essential in agroecosystems and bioinoculant development. The leaf endophytic Pseudomonas protegens E1BL2 was previously isolated from giant Jala maize, which is a native Zea mays landrace of Nayarit, Mexico. Using different Mexican maize landraces, this work evaluated the strain's plant growth promotion and biocontrol against eight phytopathogenic fungi in vitro and greenhouse conditions. Also, a plant field trial was conducted on irrigated fields using the hybrid maize Supremo. The grain productivity in this assay increased compared with the control treatment. The genome analysis of P. protegens E1BL2 showed putative genes involved in metabolite synthesis that facilitated its beneficial roles in plant health and environmental adaptation (bdhA, acoR, trpE, speE, potA); siderophores (ptaA, pchC); and extracellular enzymes relevant for PGPB mechanisms (cel3, chi14), protection against oxidative stress (hscA, htpG), nitrogen metabolism (nirD, nit1, hmpA), inductors of plant-induced systemic resistance (ISR) (flaA, flaG, rffA, rfaP), fungal biocontrol (phlD, prtD, prnD, hcnA-1), pest control (vgrG-1, higB-2, aprE, pslA, ppkA), and the establishment of plant-bacteria symbiosis (pgaA, pgaB, pgaC, exbD). Our findings suggest that P. protegens E1BL2 significantly promotes maize growth and offers biocontrol benefits, which highlights its potential as a bioinoculant.
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Enfermedades de las Plantas , Pseudomonas , Zea mays , Zea mays/microbiología , Zea mays/genética , Pseudomonas/genética , Pseudomonas/metabolismo , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Hongos/genética , Agricultura/métodos , Genómica/métodos , Genoma BacterianoRESUMEN
MOTIVATION: Gene retrocopies arise from the reverse transcription and genomic insertion of processed mRNA transcripts. These elements have significantly contributed to genetic diversity and novelties throughout the evolution of many species. However, the study of retrocopies has been challenging, owing to the absence of comprehensive, complete, and user-friendly databases for diverse species. RESULTS: Here, we introduce an improved version of RCPedia, an integrative database meticulously designed for the study of retrocopies. RCPedia offers an extensive catalog of retrocopies identified across 44 species, which includes 13 primates, 4 rodents, 6 chiropterans, 12 other mammals, 4 birds, turtles, lizards, frogs, zebrafish, and Drosophila. The database offers the most complete compilation of retrocopies per species, accompanied by detailed genomic annotations, expression data, and links to other data portals. Furthermore, RCPedia features a streamlined representation of data and an efficient querying system, establishing it as an invaluable tool for researchers in the fields of genomics, evolutionary biology, and transposable elements (TEs). In summary, RCPedia aims to enhance the investigation of retrocopies and their pivotal roles in shaping the genomic landscapes of diverse species. AVAILABILITY AND IMPLEMENTATION: RCPedia is available at https://www.rcpediadb.org.
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Bases de Datos Genéticas , Animales , Genómica/métodos , Elementos Transponibles de ADN , Evolución Molecular , Retroelementos , HumanosRESUMEN
The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.
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Genoma Humano , Humanos , Argentina , Chile , Variación Genética , Diversidad Cultural , Conducta Ceremonial , Indígenas Sudamericanos/genética , GenómicaRESUMEN
PURPOSE: This study aims to describe genomic characteristics of patients with metastatic prostate cancer (mPC). PATIENTS AND METHODS: This study is a retrospective, multicenter cohort study of patients with mPC and reports on genomic testing. Patients were included from 12 academic centers in five countries. RESULTS: A total of 349 patients with PC were included in this study. Most patients (209, 59.9%) were de novo metastatic. Genomic analysis was performed in 233 (66.6%) patients in the metastatic castration-resistant prostate cancer (mCRPC) setting, and only 115 (32.8%) patients had a tumor evaluation in the metastatic hormone sensitive prostate cancer scenario. The evaluation of somatic and/or germline mutations was performed through multigene panel analyses in 290 (83.09%) patients, and next-generation sequencing of BRCA1 and BRCA2 genes was performed in 59 (16.91%) patients. Analyzing the mCRPC subgroup, with a median follow-up of 15.6 months (IQR, 14-19.06), the median progression-free survival (PFS) was not reached (NR) and the PFS at 16 months was 58.7% (95% CI, 50.8 to 67.8). When comparing patients with BRCA mutations with those who are not BRCA-mutated in the mCRPC scenario, the median PFS was NR (95% CI, 14 to NR) and 26.3 months (95% CI, 16.7 to 36.5; P = .2), respectively. Two of six patients with BRCA mutations were treated with targeted therapies (poly-ADP-ribose polymerase inhibitors). CONCLUSION: Our study, to the best of our knowledge, represents one of the larger data sets for somatic testing in patients with PC in Latin America (LATAM). It adds valuable information to the growing body of knowledge about the genomic landscape of advanced PC in real-world daily practice scenarios in LATAM countries, which are not always well-represented in large-scale randomized clinical trials.
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Genómica , Neoplasias de la Próstata Resistentes a la Castración , Humanos , Masculino , Estudios Retrospectivos , Anciano , Persona de Mediana Edad , América Latina/epidemiología , Neoplasias de la Próstata Resistentes a la Castración/genética , Neoplasias de la Próstata Resistentes a la Castración/patología , Neoplasias de la Próstata Resistentes a la Castración/mortalidad , Neoplasias de la Próstata/genética , Neoplasias de la Próstata/patología , Neoplasias de la Próstata/mortalidad , Secuenciación de Nucleótidos de Alto Rendimiento , Proteína BRCA2/genética , Mutación , Mutación de Línea GerminalRESUMEN
The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.
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Águilas , Genoma , Animales , Águilas/genética , Femenino , Elementos Transponibles de ADN/genética , Filogenia , Evolución Molecular , Retroelementos/genética , Genómica/métodosRESUMEN
BACKGROUND: Sheep farming is growing substantially in Brazil, driven by the increasing demand for sheep meat. This rising demand has heightened the focus on sheep, making them the subject of numerous studies, including those centered on genetic analysis. A notable research area involves Pantaneiro sheep, which are indigenous to the Pantanal region of Mato Grosso do Sul and other locations. These sheep are of particular interest due to their adaptation to the unique environmental conditions of the Pantanal, a floodplain characterized by its distinctive climatic and ecological features. This study primarily aimed to conduct a comprehensive genomic analysis of Pantanal sheep subjected to natural selection within the Pantanal region and compare different sample herds using methodological approaches. METHODS: Genomic analysis was performed to examine genetic diversity and structure via GGP50K single nucleotide polymorphism (SNP) analysis. A sample of 192 adult sheep over 4 years old was categorized into seven populations based on location: Six populations comprised Pantaneiro sheep with one Texel sheep population. Outlier SNPs were assessed to pinpoint regions under natural selection, with comparisons between the Pantaneiro and the commercial Texel breeds. All data analyses were conducted using the R programming language, employing specialized genetic analysis packages. These outlier SNPs were detected using three methodologies, PCAdapt, OutFLANK, and FDIST2/fsthet, with false discovery rate (FDR) corrections applied to ensure result accuracy. Each method was evaluated, and the genes associated with the identified SNPs were cross-referenced with the most recent sheep genome database, focusing specifically on genes with known phenotypic traits. RESULTS: Analysis of a sample comprising 192 adult individuals revealed greater genetic variability within the Pantaneiro breed than the Texel breed, highlighting the adaptation of the Pantaneiro breed to the unique Pantanal environment. Conversely, the Texel breed exhibited significantly higher levels of inbreeding, attributed to its controlled breeding practices. Outlier SNPs were detected with notable variation across different methodologies, underscoring the importance of FDR correction in ensuring the reliability and concentration of identified outliers. These outlier SNPs facilitated the identification of genes associated with key phenotypic traits, including hair growth, tissue regeneration, pigmentation regulation, and muscle capacity. CONCLUSION: The integrated analysis of methodologies demonstrated significant efficiency in elucidating the genomic landscape of Pantanal sheep, highlighting the genetic richness inherent in sheep from the Pantanal region of Mato Grosso do Sul. The techniques employed effectively identified outlier SNPs associated with phenotypically relevant genes. These findings, which reveal greater genetic variability and adaptability, underscore the potential of these animals for future research and their significance within Brazilian sheep farming. The Texel breed served as a valuable comparative group, illustrating the limited genetic variability in highly controlled breeding environments.
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Polimorfismo de Nucleótido Simple , Selección Genética , Animales , Ovinos/genética , Brasil , Genómica , Variación Genética/genética , Cruzamiento , Genoma/genéticaRESUMEN
Escherichia coli is a frequent pathogen isolated from bloodstream infections. This study aimed to characterize the genetic features of EC092, an E. coli strain isolated from bacteremia that harbors enteroaggregative E. coli (EAEC) genetic markers, indicating its hybrid pathogenic potential. Whole-genome sequencing showed that EC092 belongs to phylogroup B1, ST278, and serotype O165:H4. Genes encoding virulence factors such as fimbriae, toxins, iron-uptake systems, autotransporter proteins (Pet, Pic, Sat, and SepA), and secretion systems were detected, as well as EAEC virulence genes (aggR, aatA, aaiC, and aap). EC092 was found to be closely related to the other EAEC prototype strains and highly similar in terms of virulence to three EAEC strains isolated from diarrhea. The genomic neighborhood of pet, pic, sat, sepA, and the EAEC virulence genes of EC092 and its three genetically related fecal EAEC strains showed an identical genomic organization and nucleotide sequences. Also, EC092 produced and secreted Pet, Pic, Sat, and SepA in the culture supernatant and resisted the bactericidal activity of normal human serum. Our results demonstrate that the strain EC092, isolated from bacteremia, is a hybrid pathogenic extraintestinal E. coli (ExPEC)/EAEC with virulence features that could mediate both extraintestinal and intestinal infections.
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Bacteriemia , Infecciones por Escherichia coli , Escherichia coli , Genoma Bacteriano , Factores de Virulencia , Humanos , Bacteriemia/microbiología , Escherichia coli/genética , Escherichia coli/patogenicidad , Factores de Virulencia/genética , Infecciones por Escherichia coli/microbiología , Secuenciación Completa del Genoma , Virulencia/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Filogenia , Genómica/métodosRESUMEN
The relative importance of genetic drift and local adaptation in facilitating speciation remains unclear. This is particularly true for seabirds, which can disperse over large geographic distances, providing opportunities for intermittent gene flow among distant colonies that span the temperature and salinity gradients of the oceans. Here, we delve into the genomic basis of adaptation and speciation of banded penguins, Galápagos (Spheniscus mendiculus), Humboldt (Spheniscus humboldti), Magellanic (Spheniscus magellanicus), and African penguins (Spheniscus demersus), by analyzing 114 genomes from the main 16 breeding colonies. We aim to identify the molecular mechanism and genomic adaptive traits that have facilitated their diversifications. Through positive selection and gene family expansion analyses, we identified candidate genes that may be related to reproductive isolation processes mediated by ecological thermal niche divergence. We recover signals of positive selection on key loci associated with spermatogenesis, especially during the recent peripatric divergence of the Galápagos penguin from the Humboldt penguin. High temperatures in tropical habitats may have favored selection on loci associated with spermatogenesis to maintain sperm viability, leading to reproductive isolation among young species. Our results suggest that genome-wide selection on loci associated with molecular pathways that underpin thermoregulation, osmoregulation, hypoxia, and social behavior appears to have been crucial in local adaptation of banded penguins. Overall, these results contribute to our understanding of how the complexity of biotic, but especially abiotic, factors, along with the high dispersal capabilities of these marine species, may promote both neutral and adaptive lineage divergence even in the presence of gene flow.
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Selección Genética , Spheniscidae , Animales , Spheniscidae/genética , Genómica , Especiación Genética , Flujo Génico , Genoma , Aislamiento ReproductivoRESUMEN
The basidiomycete fungus Leucoagaricus gongylophorus is able to grow in the fungus garden of leaf-cutter ants. This mutualistic interaction has driven the evolutionary adaptation of L. gongylophorus, shaping its metabolism to produce enzymes adept at lignocellulosic biomass degradation. In this study, we undertook the comprehensive sequencing, assembly, and functional annotation of the genome of L. gongylophorus strain LEU18496, mutualistic fungus of the Atta mexicana. Our genomic analyses revealed a distinctive bimodal nature to the genome: a predominant region characterized by AT enrichment and low genetic density, alongside a smaller region exhibiting higher GC content and higher genetic density. The presence of transposable elements (TEs) within the AT-enriched region suggests genomic compartmentalization, facilitating differential evolutionary rates. With a gene count of 6748, the assembled genome of L. gongylophorus LEU18496 surpasses previous reports for this fungal species. Inspection of genes associated with central metabolism unveiled a remarkable abundance of carbohydrate-active enzymes (CAZymes) and fungal oxidative lignin enzymes (FOLymes), underscoring their pivotal roles in the life cycle of this fungus.
Asunto(s)
Genoma Fúngico , Anotación de Secuencia Molecular , Simbiosis , Simbiosis/genética , Animales , Genómica/métodos , Elementos Transponibles de ADN/genética , Agaricales/genética , Composición de Base , Filogenia , Hormigas/genética , Hormigas/microbiología , Basidiomycota/genéticaRESUMEN
Fusarium head blight (FHB) is a major disease of wheat and barley worldwide and is caused by different species in the genus Fusarium, Fusarium graminearum being the most important. We conducted population genomics analyses using SNPs obtained through genotyping by sequencing of over 500 isolates of F. graminearum from the US Upper Midwest, New York, Louisiana, and Uruguay. PCA and STRUCTURE analyses group our isolates into four previously described populations: NA1, NA2, Southern Louisiana (SLA) and Gulf Coast (GC). Some isolates were not assigned to populations because of mixed ancestry. Population structure was associated with toxin genotype and geographic origin. The NA1, NA2, and SLA populations are differentiated (FST 0.385 - 0.551) but the presence of admixed isolates indicates that the populations are not reproductively isolated. Patterns of linkage disequilibrium (LD) decay suggest frequent recombination within populations. Fusarium graminearum populations from the US have great evolutionary potential given the high recombination rate and a large proportion of admixed isolates. The NA1, NA2, and Southern Louisiana (SLA) populations separated from their common ancestral population roughly at the same time in the past and are evolving with moderate levels of subsequent gene flow between them. Genome-wide selection scans in all three populations revealed outlier regions with the strongest signatures of recent positive natural selection. These outlier regions include many genes with unknown function and some genes with known roles in plant-microbe interaction, fungicide/drug resistance, cellular transport and genes that are related to cellular organelles. Only a very small proportion of outlier regions are shared as outliers among the three populations, suggesting unique host-pathogen interactions and environmental adaptation.
Asunto(s)
Fusarium , Desequilibrio de Ligamiento , Enfermedades de las Plantas , Polimorfismo de Nucleótido Simple , Fusarium/genética , Fusarium/clasificación , Fusarium/aislamiento & purificación , Enfermedades de las Plantas/microbiología , Polimorfismo de Nucleótido Simple/genética , Triticum/microbiología , Genoma Fúngico/genética , Américas , Genotipo , Genómica , Metagenómica , Hordeum/microbiología , UruguayRESUMEN
Bacteria can solubilize phosphorus (P) through the secretion of low-molecular-weight organic acids and acidification. However, the genes involved in the production of these organic acids are poorly understood. The objectives of this study were to verify the calcium phosphate solubilization and the production of low-molecular-weight organic acids by diverse genera of phosphate solubilizing bacterial strains (PSBS); to identify the genes related to the synthesis of the organic acids in the genomes of these strains and; to evaluate growth and nutrient accumulation of maize plants inoculated with PSBS and fertilized with Bayóvar rock phosphate. Genomic DNA was extracted for strain identification and annotation of genes related to the organic acids production. A greenhouse experiment was performed with five strains plus 150 mg dm- 3 P2O5 as Bayóvar rock phosphate (BRP) to assess phosphate solubilization contribution to maize growth and nutrition. Paraburkholderia fungorum UFLA 04-21 and Pseudomonas anuradhapurensis UFPI B5-8A solubilized over 60% of Ca phosphate and produced high amounts of citric/maleic and gluconic acids in vitro, respectively. Eleven organic acids were identified in total, although not all strains produced all acids. Besides, enzymes related to the organic acids production were found in all bacterial genomes. Plants inoculated with strains UFPI B5-6 (Enterobacter bugandensis), UFPI B5-8A, and UFLA 03-10 (Paenibacillus peoriae) accumulated more biomass than the plants fertilized with BRP only. Strains UFLA 03-10 and UFPI B5-8A increased the accumulation of most macronutrients, including P. Collectively, the results show that PSBS can increase maize growth and nutrient accumulation based on Bayóvar rock phosphate fertilization.
Asunto(s)
Bacterias , Fosfatos , Zea mays , Zea mays/crecimiento & desarrollo , Zea mays/microbiología , Zea mays/metabolismo , Fosfatos/metabolismo , Bacterias/genética , Bacterias/metabolismo , Bacterias/clasificación , Fosfatos de Calcio/metabolismo , Microbiología del Suelo , Genoma Bacteriano , Desarrollo de la Planta , Solubilidad , Gluconatos/metabolismo , Genómica , Fósforo/metabolismo , FilogeniaRESUMEN
Herbicide-resistant Conyza spp. are a threat to many crops. These widespread weeds are closely related species and often cooccur. To characterize the origins of their resistance and the mechanisms underlying their spread, we assessed the genomic variation in glyphosate-resistant Conyza spp. in Brazil. Twenty populations were sampled from soybean fields across four macroregions (MRSs). A genotyping-by-sequencing study resulted in 2,998 single-nucleotide polymorphisms (SNPs) obtained for C. bonariensis (L.) and the closely related C. sumatrensis (Retz) E. Walker. Higher genomic diversity (π) and heterozygosity (HO/HE) and lower inbreeding coefficient (FIS) values were detected in populations of Conyza spp. from MRS 1 (southern) than in those from other MRSs. Strong genomic structure clustered individuals into three groups (FST = 0.22; p value = 0.000) associated with the MRSs. Thus, resistance to glyphosate originated from independent selection in different MRSs across Brazil. Our dataset supports the occurrence of intraspecific gene flow in Brazil and identified individuals of C. bonariensis that did not group within species. These findings suggest that allelic introgressions within and among species have impacted the evolution and spread of resistance to glyphosate in Conyza spp. We discuss how to mitigate new resistance cases, particularly for the released stacked traits herbicide tolerance in soybeans.