Diversity of Colletotrichum species associated with torch ginger anthracnose.

Anthracnose caused by Colletotrichum species is one of the most important diseases of torch ginger. The disease leads to loss of aesthetic and commercial value of torch ginger stems. This study aimed to characterize Colletotrichum species associated with torch ginger anthracnose in the production areas of Pernambuco and Ceará. A total of 48 Colletotrichum isolates were identified using molecular techniques. Pathogenicity tests were performed on torch ginger with representative isolates. Phylogenetic analyses based on seven loci-DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), intergenic spacer between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a hypothetical protein (GAP2-IGS), glutamine synthetase (GS), and ß-tubulin (TUB2)-revealed that they belong to five known Colletotrichum species, namely, C. chrysophilum, C. fructicola, C. siamense, C. theobromicola, and C. tropicale, and three newly discovered species, described here as C. atlanticum, C. floscerae, and C. zingibericola. Of these, C. atlanticum was the most dominant. Pathogenicity assays showed that all isolates were pathogenic to torch ginger bracts. All species are reported for the first time associated with torch ginger in Brazil. The present study contributes to the current understanding of the diversity of Colletotrichum species associated with anthracnose on torch ginger and demonstrates the importance of accurate species identification for effective disease management strategies.

The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases.

SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.

Comparative genomics and phylogenomics of the Ralstonia solanacearum Moko ecotype and its symptomatological variants.

Banana tree bacterial wilt is caused by the Ralstonia solanacearum Moko ecotype. These strains vary in their symptom progression in banana, and are classified as typical Moko variants (phylotype IIA and IIB strains from across Central and South America), Bugtok variant (Philippines), and Sergipe facies (the states of Sergipe and Alagoas, Brazil). This study used comparative genomic and phylogenomic approaches to identify a correlation between the symptom progression of the Moko ecotypes based on the analysis of 23 available genomes. Average nucleotide identity and in silico DNA-DNA hybridization revealed a high correlation (>96% and >78%, respectively) between the genomes of Moko variants. Pan-genome analysis identified 21.3% of inheritable regions between representatives of the typical Moko and Sergipe facies variants, which could be traced to an abundance of exclusive homolog clusters. Moko ecotype genomes shared 1,951 orthologous genes, but representatives with typical symptoms did not display unique orthologues. Moreover, Bugtok disease and Sergipe facies genomes did not share any unique genes, suggesting convergent evolution to a shared symptom progression. Overall, genomic and phylogenomic analyses were insufficient to differentiate the Moko variants based on symptom progression.

Phytochemistry and Biological Activities of Amburana cearensis (Allemão) ACSm.

Amburana cearensis (Allemão) ACSm. belongs to the Fabaceae family and occurs in the Brazilian semiarid, Argentina, Paraguay, Bolivia, and Peru. Numerous studies that portray its ethnobotany, use in popular medicine, chemical composition, and biological activities exist in the literature. This review aimed to provide an overview of the chemical composition, ethnopharmacology, and biological activities associated with A. cearensis and its isolated constituents. Information was collected from internet searches in the Scopus, Medline, PubMed, Google Scholar, and ScienceDirect databases were performed covering publications from 1997-2020. An ethnopharmacological literature analysis revealed that A. cearensis is used to treat a wide range of respiratory disorders in addition to intestinal, circulatory, and inflammatory problems. Coumarins, flavonoids, phenolic glycosides, phenolic acids, phenylpropanoid derivatives, and triterpenoids, among others, have been reported as active compounds, with High-Performance Liquid Chromatography (HPLC) being the main analytical technique used. The A. cearensis extracts and compounds presented several biological activities, including antimicrobial, antinociceptive, anti-inflammatory, antioxidant, neuroprotective, and myorelaxant activities, among others. This review provides a useful bibliography for future investigations and A. cearensis applications; however, future studies should focus on its toxic effects and the mechanisms of action of its extracts and isolated constituents to guide clinical applications.

EntroPhylo: An entropy-based tool to select phylogenetic informative regions and primer design.

We present a novel entropy-based computational tool that selects phylogenetic informative genomic regions associated with degenerate primer design. This tool identifies proper phylogenetic markers and proposes suitable degenerate primers to amplify and sequence them. The algorithm calculates the entropy value per site, and the selected region is used for primer design. In order to evaluate the tool, sequences of bovine papillomavirus L1 gene were obtained. Once the molecular region was selected, the primers were designed by the software and used in a PCR reaction for viral detection. Three positive samples were tested with four different concentrations, and it was possible to detect the virus in all samples. The results show the applicability of a tool that can select informative regions for phylogenetic analysis and design primers to amplify and sequence these regions, becoming relevant for several studies focusing on pathogen detection, as well as phylogenetic and genetics studies of populations.

Genomic sequencing of different sequevars of Ralstonia solanacearum belonging to the Moko ecotype.

Banana vascular wilt or Moko is a disease caused by Ralstonia solanacearum. This study aimed to sequence, assemble, annotate, and compare the genomes of R. solanacearum Moko ecotypes of different sequevar strains from Brazil. Average nucleotide identity analyses demonstrated a high correlation (> 96%) between the genome sequences of strains CCRMRs277 (sequevar IIA-24), CCRMRs287 (IIB-4), CCRMRs304 (IIA-24), and CCRMRsB7 (IIB-25), which were grouped into phylotypes IIA and IIB. The number of coding sequences present in chromosomes and megaplasmids varied from 3,070 to 3,521 and 1,669 to 1,750, respectively. Pangenome analysis identified 3,378 clusters in the chromosomes, of which 2,604 were shared by all four analyzed genomes and 2,580 were single copies. In megaplasmids, 1,834 clusters were identified, of which 1,005 were shared by all four genomes and 992 were identified as single copies. Strains CCRMRsB7 and CCRMRs287 differed from the others by having unique clusters in both their chromosomes and megaplasmids, and CCRMRsB7 possessed the largest genome among all Moko ecotype strains sequenced to date. Therefore, the genomic information obtained in this study provides a theoretical basis for the identification, characterization, and phylogenetic analysis of R. solanacearum Moko ecotypes.

Genomic sequencing of two isolates of Ralstonia solanacearum causing Sergipe facies and comparative analysis with Bugtok disease isolates.

Ralstonia solanacearum is the causal agent of Moko disease in bananas, which in the state of Sergipe in northeastern Brazil causes "Sergipe facies". This disease induces atypical symptoms similar to those of Bugtok disease in the Philippines. This study was conducted to sequence, assemble, and annotate the genomes of the Sergipe facies-causing isolates SFC and IBSBF2570 (sequevar IIA-53) and compare their genomes with two representative isolates causing Bugtok disease. The genomes were sequenced and assembled, resulting in lengths of 5.58 Mb (SFC) and 5.46 Mb (IBSBF2570) in 185 and 174 contigs, respectively. The isolates of Sergipe facies and Bugtok disease showed similarities in their gene contents. We identified 5,668 information clusters, 3,752 of which were shared by all genomes (core genes). Moreover, 3,585 single-copy genes were identified. Isolates causing Bugtok disease exclusively shared 266 more information clusters than the isolates causing Sergipe facies. These results suggest that Sergipe facies and Bugtok disease isolates show high genomic similarity. However, the similarity is even greater between the Bugtok disease isolates. This may be because of their longer period of interaction compared to Sergipe facies isolates.

Draft genome assembly of Colletotrichum musae, the pathogen of banana fruit.

Colletotrichum musae is an important cosmopolitan pathogenic fungus that causes anthracnose in banana fruit. The entire genome of C. musae isolate GM20 (CMM 4420), originally isolated from infected banana fruit from Alagoas State, Brazil, was sequenced and annotated. The pathogen genomic DNA was sequenced on HiSeq Illumina platform. The C. musae GM20 genome has 50,635,197 bp with G + C content of 53.74% and in its present assembly has 2763 scaffolds, harboring 13,451 putative genes with an average length of 1626 bp. Gene prediction and annotation was performed by Funannotate pipeline, using a pattern for gene identification based on BUSCO.

Canine ß-defensin-1 (CBD1) gene as a possible marker for Leishmania infantum infection in dogs.

BACKGROUND: Canine leishmaniasis caused by Leishmania infantum is a parasitic disease of great veterinary significance. Some dogs infected by L. infantum may mount a strong cellular immune response and clear the infection, while others may respond with exaggerated antibody production against the parasite and develop an overt disease, which may be fatal, if left untreated. The initial factors triggering the polarization of the immune response towards a predominantly T-helper 1 or T-helper 2 cytokines, as well as the markers of resistance and susceptibility to L. infantum infection and disease development in dogs, are not fully understood. Herein, we assessed the association between single nucleotide polymorphisms (SNPs) in the canine ß-defensin-1 (CBD1) gene and the infection by L. infantum in two dog populations from Brazil (Sobral in Ceará State and São Raimundo Nonato in Piauí State) and one dog population from Italy. RESULTS: A total of 387 dogs were assessed for L. infantum by real time PCR and 34.6% of them were positive. In CBD1 gene sequences from these positive dogs, nine polymorphic sites were detected, but only SNPs 3, 4, 7 and 8 were associated with L. infantum, in dogs from southern Italy. No association was found with dogs from Brazil. CONCLUSION: This study sets the basis for further studies on the usefulness of CBD1 as a marker of L. infantum infection susceptibility in dogs.

Analysis of the genetic structure of allopatric populations of Lutzomyia umbratilis using the period clock gene.

In South America, Lutzomyia umbratilis is the main vector of Leishmania guyanensis, one of the species involved in the transmission of American tegumentary leishmaniasis. In Brazil, L. umbratilis has been recorded in the Amazon region, and an isolated population has been identified in the state of Pernambuco, Northeastern region. This study assessed the phylogeographic structure of three allopatric Brazilian populations of L. umbratilis. Samples of L. umbratilis were collected from Rio Preto da Eva (north of the Amazon River, Amazonas), from Manacapuru (south of the Amazon River), and from the isolated population in Recife, Pernambuco state. These samples were processed to obtain sequences of the period gene. Phylogenetic analysis revealed the presence of two distinct monophyletic clades: one clade comprised of the Recife and Rio Preto da Eva samples, and one clade comprised of the Manacapuru samples. Comparing the Manacapuru population with the Recife and Rio Preto da Eva populations revealed high indices of interpopulational divergence. Phylogenetic analysis indicated that geographical distance and environmental differences have not modified the ancestral relationship shared by the Recife and Rio Preto da Eva populations. Genetic similarities suggest that, in evolutionary terms, these populations are more closely related to each other than to the Manacapuru population. These results confirm the existence of an L. umbratilis species complex composed of at least two incipient species.

Genetic structuring and fixed polymorphisms in the gene period among natural populations of Lutzomyia longipalpis in Brazil.

BACKGROUND: Even one hundred years after being originally identified, aspects of the taxonomy of the sand fly Lutzomyia longipalpis, the principal vector of Leishmania infantum in the Americas, remain unresolved for Brazilian populations of this vector. The diversity of morphological, behavioral, biochemical, and ethological characters, as well as the genetic variability detected by molecular markers are indicative of the presence of a complex of species. METHODS: In this study, a 525 bp fragment of the period gene was used to evaluate sympatric populations of L. longipalpis. A combination of probabilistic methods such as maximum likelihood and genetic assignment approach to investigate sympatric species of L. longipalpis were applied in three populations of Northeast Brazil. RESULTS: Fixed polymorphisms in geographically isolated populations of L. longipalpis from two localities in the state of Ceará and one in the state of Pernambuco, Brazil, was identified in a 525 bp fragment of the gene period (per). Our results suggest a direct relationship between the number of spots found in males' tergites and the genetic variation in cryptic species of L. longipalpis. The fragment used in this study revealed the nature of the ancestral morphotype 1S. CONCLUSION: New polymorphisms were identified in the gene per which can be used as a genetic barcode to sympatric taxonomy of L. longipalpis. The per gene fragment confirmed the presence of two siblings species of L. longipalpis in Sobral and showed that these same species are present in two other localities, representing an expansion within the L. longipalpis species complex with regards to the states of Ceará and Pernambuco.

Meta-analysis of Brazilian genetic admixture and comparison with other Latin America countries.

OBJECTIVES: This study aims at performing a systematic review and meta-analysis with the studies of genetic admixture inference of Brazilian population and to compare these results with the genetic admixture levels in other Latin American countries. METHODS: We searched for articles regarding the estimation of Brazilian genetic admixture published between 1980 and 2014 that used autosomal markers. Then, conducted meta-analyses at the whole-country and regional level. Finally, we compared the results of Brazil with other estimates from other South, Central and North American countries. RESULTS: We analyzed data from 25 studies in 38 different Brazilian populations. European (EUR) ancestry is the major contributor to the genetic background of Brazilians, followed by African (AFR), and Amerindian (AMR) ancestries. The pooled ancestry contributions were 0.62 EUR, 0.21 AFR, and 0.17AMR. The Southern region had a greater EUR contribution (0.77) than other regions. Individuals from the Northeast (NE) region had the highest AFR contribution (0.27) whereas individuals from the North regions had more AMR contribution (0.32). In the Latin America context, Brazil has the 5th high EUR contribution, the 12th for the AFR component and the 10th for the AMR ancestry. CONCLUSIONS: Admixture proportions vary greatly among Brazilian populations and also through Latin America. More studies in the Center-West, North and NE regions are needed to capture a more complete picture of the genomic ancestry of Brazil.

Importância da distribuição geográfica dos vetores da doença de chagas em Pernambuco, Brasil, em 2012 / The importance of the geographical distribution of Chagas disease vectors in Pernambuco during 2012

Objetivos: Ressaltar a importância da distribuição geográfica e do comportamento dos vetores dadoença de Chagas no estado de Pernambuco. Métodos: O material analisado incluiu 100 por cento dosinsetos infectados por Trypanosoma sp. e 40 por cento dos insetos negativos, examinados no Laboratório deEndemias para confirmação taxonômica, pesquisa do parasito nas fezes dos triatomíneos e Controleda Qualidade na confirmação do diagnóstico. Resultados: Foram examinados 3.323 triatomíneos.A infecção natural por tripanossomatídeos foi detectada em 21,3 por cento dos exemplares. Triatomabrasiliensis foi a espécie mais frequente no intradomicílio (24,3 por cento), Triatoma pseudomaculata(14,9 por cento) e Panstrongylus megistus apresentaram proporcionalmente taxa de infecção naturalsuperior às demais (40,8 por cento) no peridomicílio. Conclusão: O conhecimento atualizado da distribuiçãogeográfica dos vetores da doença de Chagas é importante para fundamentar ações integradas entreos serviços de saúde, o que contribui para a vigilância entomológica no controle dos triatomíneos.

Objectives: To underscore the importance of geographic distribution and behavior of vectors ofChagas disease in the state of Pernambuco. Methods: The material analyzed included 100 percent of theinsects infected with Trypanosoma spp., and 40 percent of negative insects, examined at the EndemicDisease Laboratory for taxonomic confirmation, searching for the parasite in feces of the insects,with Quality Control to confirm the diagnosis. Results: A total of 3,323 triatomines. Naturalinfection by trypanosomes was detected in 21.3 percent of the specimens. Triatoma brasiliensis wasthe most frequent intradomiciliary species (24.3 percent), outside the home Triatoma pseudomaculata(14.9 percent) and Panstrongylus megistus had a natural infection rate proportionally superior to the others(40.8 percent). Conclusion: The current knowledge of the geographical distribution of Chagas diseasevectors is important as a platform to integrate actions between health services, contributing to theentomological surveillance and control of the insects.

Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) in the State of Pernambuco.

INTRODUCTION: Phlebotomine sand flies are small insects of great medical relevance. This article presents an updated list of the phlebotomine sand flies occurring in the State of Pernambuco, Brazil. METHODS: A review of literature published since the 1940s up to May 2010 was conducted and voucher material deposited in reference collections were studied. RESULTS: A total of 37 phlebotomine species have previously been reported as occurring in Pernambuco, but the record of six species needs confirmation. CONCLUSIONS: This work provides an updated list of phlebotomine sand flies of Pernambuco, with some notes on their taxonomy, ecology, distribution and epidemiological relevance.

Phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) in the State of Pernambuco / Flebotomíneos (Diptera: Psychodidae: Phlebotominae) no Estado de Pernambuco

INTRODUCTION: Phlebotomine sand flies are small insects of great medical relevance. This article presents an updated list of the phlebotomine sand flies occurring in the State of Pernambuco, Brazil. METHODS: A review of literature published since the 1940s up to May 2010 was conducted and voucher material deposited in reference collections were studied. RESULTS: A total of 37 phlebotomine species have previously been reported as occurring in Pernambuco, but the record of six species needs confirmation. CONCLUSIONS: This work provides an updated list of phlebotomine sand flies of Pernambuco, with some notes on their taxonomy, ecology, distribution and epidemiological relevance.

INTRODUÇÃO: Flebotomíneos são pequenos insetos de grande importância médica e veterinária. Este artigo apresenta uma lista atualizada dos flebotomíneos que ocorrem no Estado de Pernambuco, Brasil. MÉTODOS: Uma revisão da literatura publicada desde a década de 40 até maio de 2010 foi realizada e material testemunho depositado em coleções de referência foi estudado. RESULTADOS: Um total de 37 espécies de flebotomíneos foram previamente relatadas como presentes em Pernambuco, mas o registro de seis delas necessita de confirmação. CONCLUSÕES: Esse trabalho fornece uma lista atualizada de flebotomíneos de Pernambuco, com algumas notas sobre a sua taxonomia, ecologia, distribuição e relevância epidemiológica.

The pgm locus and pigmentation phenotype in Yersinia pestis

The pigmentation (pgm) locus is a large unstable area of the Yersinia pestis chromosome composed of a segment of iron acquisition (HPI) linked to a pigmentation segment. In this work we examined the mobility of HPI and the pigmentation segment in three Y. pestis isolates using successive subcultures on Congo red agar (CRA) plates. Strain P. CE 882 was shown to be highly stable while strains P. Exu 340 and P. Peru 375 dissociated into several phenotypes, PCR analysis showing evidence of changes in the pgm locus of the derived cultures. Strains P. Exu 340 and P. Peru 375 produced previously unreported cultures positive for the pesticin/yersiniabactin outer membrane receptor (psn+) but negative for the iron-regulated protein (irp2-), suggesting the occurrence of rearrangements in this chromosomal region and either a sequential loss or the loss of separated segments. These results provide evidence that besides deletion en bloc, specific rearrangements are also involved in the deletion events for that locus.

Variabilidade genética de marcadores RAPD-PCR e caracterização in silico de etiquetas de genes expressos (ESTs) de Lutzomyia longipalpis (diptera: psychodidae) / Genetic variability of RAPD-PCR markers and characterization in silico of express gene markers (EST) of Lutzomyia longipaipis (diptera: psychodidae)

A leishmaniose visceral é uma endemia de regiões de clima tropical e sub-tropical do mundo, acometendo milhares de pessoas a cada ano. Apresenta como agente etiológico a Leishmania chagasi, protozoário da familia Trypanosomatidade transmitido os seres humanos pela picada das fêmeas do flebotomíneo LUtzomyia longipalpis. A despeito de sua reconhecida importância epidemiológica, o número de trabalhos envolvendo a aplicação de técnicas de biologia molecular na análise deste inseto ainda é bastante reduzido. Neste trabalho, descreve-se a utilização das técnicas do RAPD-PCR e do seqüenciamento de genes expressos (ESTs) com o objetivo de identificar marcadores moleculares que possam ser utilizados tanto em estudos de genética de populações de L. longipalpis, quanto na identificação de genes que possam estar envolvidos nos processos que determinam a relaçãoi destes insetos com os agentes etiológicos que eles transmitem. Foram investigados os polimorfismos de 17 locos RAPD-PCR em 7 populações de L. longipalpis do Nordeste brasileiro. O grau de diferenciação genética entre as populações foi determinado a partir da estimativa dos índices de fixação Fst e 0 que evidenciaram a existência de um grau moderado de estruturação genética, decorrente do ioslamento geográfico entre elas, Paralelamente ao estudo da estrutura genètica das pouplações de L. longipalpis, também foram analisadas 116 etiquetas de digestivos de espécimes de L. longipalpis artificialmente infectados com L. chagasi. Do total de seqüências de insetos já descritas na literatura, com a maioria apresentando similaridade com genes de Drosophila melanogaster. O nível de redundância das ESTs foi relativamente baixo, com a maior parte das seqüências (87,67 por cento) sendo encontrada uma única vez, indicando um bom nível de representatividade da biblioteca estudada. Dentre os supostos produtos gênicos identificados, os relacionados com a síntese de proteínas apseguidos das proteínas ribossomais e enzimas digestivas, com ambas representando 8,57 por cento do total de seqüências analisadas. As informações produzidas neste trabalho demonstraram a viabilidade da utilização do seqüenciamento de genes expressos na identificação de genes da L. longipalpis, servindo como referencial para o estabelecimento de experimentos voltados para a caracterização in vivo dos produtos gênicos encontrados, a exemplo do que já vem sendo em outras espécies de insetos vetores.