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The evaluation of genome size has emerged as a resource for populational, biogeographic, and evolutionary interpretations. Still, little has been recorded on the size of the genomes of decapod crustaceans, mainly freshwater species. Using flow cytometry, we aimed to provide new data on the genome size of the freshwater crabs Trichodactylus fluviatilis Latreille, 1828 and T. petropolitanus (Göldi, 1886) in São Paulo state, southern Brazil. We analyzed 12 individuals with a c-value of 8.0–9.6 picograms. We observed a tendency for freshwater crabs with direct development to have a higher genome-size value than those decapods with indirect development, which links the possible relationship of genome size with the developmental pattern. [ABSTRACT FROM AUTHOR]

This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders. [ABSTRACT FROM AUTHOR]

Cashew (Anacardium occidentals) angular leaf spot is caused by pigmented and nonpigmented strains of Xanthomonas citri pv. anacardii, which have been isolated from infected plants in Brazil. The disease symptoms can be observed in leaves, stems, and fruits. Given that infection in young fruits results in fruits unsuitable for commercialization, angular leaf spot represents a serious threat to the cashew crop in Brazil. Here, we report the genomic sequencing of seven pigmented strains of X. citri pv. anacardii, obtained from the leaves of cashew trees from Sao Paulo state, Brazil, in 2009. The construction of the libraries was carried out according to the manufacturer, and whole-genome sequencing was performed using the Illumina HiSeq 2500 platform. Genome size, number of coding sequences, largest contig length, and N50 ranged from 4,996,984 to 5,003,485 bp, 4,621 to 4,643 bp, 212,513 to 362,232 bp, and 113,582 to 141,003 bp, respectively. GC content and RNA numbers were 64.68% and 54, respectively, for all strains. ANIm and dDDH analyses showed values above 99.5 and 92.1% among these strains and the non-pigmented pathotype strain of X. citri pv. anacardii (IBSBF2579PT). A maximum likelihood tree built with 2,708 core genes grouped all X. citri pv. anacardii strains in the same clade, with a 100% bootstrap. These resources will contribute in a relevant way to help understand the ecological, taxonomic, evolutionary, pathogenicity, and virulence aspects of X. citri pv. anacardii, which will be useful for the study and development of techniques for managing cashew angular leaf spot. [ABSTRACT FROM AUTHOR]

Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events. [ABSTRACT FROM AUTHOR]

Begomoviruses are members of the family Geminiviridae, a large and diverse group of plant viruses characterized by a small circular single-stranded DNA genome encapsidated in twinned quasi-icosahedral virions. Cultivated tomato (Solanum lycopersicum L.) is particularly susceptible and is infected by .100 bipartite and monopartite begomoviruses worldwide. In Brazil, 25 tomato-infecting begomoviruses have been described, most of which are bipartite. Tomato mottle leaf curl virus (ToMoLCV) is one of the most important of these and was first described in the late 1990s but has not been fully characterized. Here, we show that ToMoLCV is a monopartite begomovirus with a genomic DNA similar in size and genome organization to those of DNA-A components of New World (NW) begomoviruses. Tomato plants agroinoculated with the cloned ToMoLCV genomic DNA developed typical tomato mottle leaf curl disease symptoms, thereby fulfilling Koch's postulates and confirming the monopartite nature of the ToMoLCV genome. We further show that ToMoLCV is transmitted by whiteflies, but not mechanically. Phylogenetic analyses placed ToMoLCV in a distinct and strongly supported clade with other begomoviruses from northeastern Brazil, designated the ToMoLCV lineage. Genetic analyses of the complete sequences of 87 ToMoLCV isolates revealed substantial genetic diversity, including five strain groups and seven subpopulations, consistent with a long evolutionary history. Phylogeographic models generated with partial or complete sequences predicted that the ToMoLCV emerged in northeastern Brazil .700 years ago, diversifying locally and then spreading widely in the country. Thus, ToMoLCV emerged well before the introduction of MEAM1 whiteflies, suggesting that the evolution of NW monopartite begomoviruses was facilitated by local whitefly populations and the highly susceptible tomato host. [ABSTRACT FROM AUTHOR]

Genome size (GS) or DNA nuclear content is considered a useful index for making inferences about evolutionary models and life history in animals, including taxonomic, biogeographical, and ecological scenarios. However, patterns of GS variation and their causes in crustaceans are still poorly understood. This study aimed to describe the GS of five Neotropical Synalpheus non-gambarelloides shrimps (S. apioceros, S. minus, S. brevicarpus, S. fritzmueller, and S. scaphoceris) and compare the C-values of all Caridea infraorder in terms of geography and phylogenetics. All animals were sampled in the coast of São Paulo State, Brazil, and GS was assessed by flow cytometry analysis (FCA). The C-values ranged from 7.89 pg in S. apioceros to 12.24 pg in S. scaphoceris. Caridean shrimps had higher GS than other Decapoda crustaceans. The results reveal a tendency of obtaining larger genomes in species with direct development in Synalpheus shrimps. In addition, a tendency of positive biogeographical (latitudinal) correlation with Caridea infraorder was also observed. This study provides remarkable and new protocol for FCA (using gating strategy for the analysis), which led to the discovery of new information regarding GS of caridean shrimps, especially for Neotropical Synalpheus, which represents the second-largest group in the Caridea infraorder. [ABSTRACT FROM AUTHOR]

The Epidendrum nocturnum Jacq. group comprises about 60 species. Nine species occur in Brazil, predominantly in the Atlantic and Amazon Forests. The group is taxonomically complex because its species are morphologically similar and not easily distinguished. The main objective of this work is to characterize their chromosome evolution and how this has affected species delimitation in Brazilian representatives of the E. nocturnum group. We used chromosome numbers, heterochromatin band patterns, and genome size variation to better understand the chromosome variation, species delimitation, and the relationship among seven representatives of this group. A new species from the Cerrado/Amazon Rainforest ecotone is described based on cytological and morphological characters. The new species, Epidendrum pareciense sp. nov., is a diploid (2n = 40), Epidendrum bahiense Rchb.f., Epidendrum carpophorum Barb.Rodr., Epidendrum micronocturnum Carnevali & G.A.Romero, Epidendrum purpureocaulis Sambin & Essers, and E. nocturnum are tetraploids (2n = 80), and Epidendrum tumuc-humaciense (Veyret) Carnevali & G.A.Romero is hexaploid (2n = 120), the last a new ploidy for the group. Heterochromatin in these species is characterized by guanine-cytosine-rich regions (cromomycin A3 (CMA+) bands) on proximal and terminal regions associated with NORs. Genome size and numbers of CMA terminal bands are directly related to ploidy, suggesting that diploidization has not yet occurred and supporting the hypothesis of a recent polyploid origin for the E. nocturnum group. [ABSTRACT FROM AUTHOR]

The stingless bee Partamona helleri (Meliponini) is distributed across the Atlantic rainforest biome in Brazil. Cytogenetic studies on P. helleri have shown a conserved diploid number and the presence of several B chromosome types. Our goal was to investigate the intraspecific karyotypic variation among 21 colonies of P. helleri from 14 different localities across four Brazilian states, using classical and molecular cytogenetics, as well as image cytometry (ICM). All populations had 2n = 34 and up to 5B chromosomes, which showed inter- and intra-population variation in number and size. C-banding evidenced the centromeric/pericentromeric heterochromatin and the partially heterochromatic B chromosomes. GA(15) microsatellite hybridized in the euchromatic arm of the A chromosomes and did not mark the B chromosomes, whereas TTAGG(6) corresponded to the telomeric sequence of the A and B chromosomes. The 18S rDNA and CMA3+ sites varied among the colonies, indicating the karyotype variability of the species. The ICM demonstrated an increase in nuclear genome size regarding the presence of B chromosomes. We highlighted the importance of population studies in species with a wide range of distributions, and how the B chromosomes contribute to the intra- and inter-population variability of P. helleri. [ABSTRACT FROM AUTHOR]

Aquimarina litoralis CCMR20 originated from the coral Mussismilia braziliensis (Sebastião Gomes Reef, Brazil, summer 2010). To gain new insights into the genomic repertoire associated with symbioses, we obtained the genome sequence of this strains using Illumina sequencing. CCMR20 has a genome size of 6.3 Mb, 32.6%GC, and 5513 genes (37 tRNA and 4 rRNA). A more fine-grained examination of the gene repertoire of CCMR20 disclosed genes engaged with symbiosis (heterotrophic carbon metabolism, CAZymes, B-vitamins group, carotenoid pigment and antioxidant molecules production). Genomic evidence further expand the possible relevance of this symbiont in the health of Mussismilia holobiont. Whole Genome Shotgun project has been deposited at DDBJ/ENA/GeneBank under the accession number WEKL00000000. [ABSTRACT FROM AUTHOR]

A new species of Macrotorus (Monimiaceae) from the Brazilian Atlantic rainforest is here described and illustrated: Macrotorus genuflexus. This species, restricted to the Poço das Antas Biological Reserve (situated in the central region of Rio de Janeiro state, Brazil), is the second in the genus Macrotorus. The new species description is based on morphological and cytogenetic (karyotype and genome size) comparative analyses. We also report a new record of Macrotorus utriculatus for the state of Bahia, confirming a potential distribution modelling prediction, and provide comments for the conservation of both species. [ABSTRACT FROM AUTHOR]

Plant evolution may be triggered by significant chromosome changes. In some plant groups, karyoevolution played an important role, influencing speciation processes. Hohenbergia comprises 48 species distributed through eastern Brazil. Previous cytological information includes few species and only chromosome counts, lacking information about genome size and more accurate karyomorphological investigation. Here, we compare cytomolecular features and genome sizes of 12 Hohenbergia spp. Besides, new measurements of genome sizes of 32 species are reported. All studied species presented 2 n = 50, a number prevalent in Bromelioideae. The genome sizes (2C) varied from 0.74 to 1.52 pg. Despite the apparent homogeneity in chromosome number and genome size in Hohenbergia , significant polymorphism was observed in regard to the distribution of CMA+/DAPI0 bands and sites of 35S and 5S rDNA in metaphase chromosomes. Seven out of 12 analysed species presented heteromorphic pairs regarding 35S rDNA and/or 5S rDNA. Hohenbergia thus shows karyotypic diversity despite the conservation in chromosome number. [ABSTRACT FROM AUTHOR]

Sixteen species of Costus s.s. are cited to Brazil, all of which can be found in the Brazilian Amazon, while only three also grow in the Atlantic Forest: C. arabicus, C. scaber, and C. spiralis. Studies of the genus from the Brazilian Atlantic Forest evidenced a distinctive fourth taxon, similar overall to C. spiralis, which is an ornithophilous species, however the flower morphology of this new taxon indicates it to be melittophilous. Hybridization and polyploidy (allopolyploidy or autopolyploidy) may play a role as an important source for evolutionary events, especially in recent speciose lineages such as Neotropical Costus. Here we investigated the evolutionary origin of this interesting Costus species using an integrative approach. This approach comprised a morphological analysis, cytogenetic analyses (chromosome counts, CMA/DAPI staining, and fluorescent in situ hybridization), genome size estimations, and a molecular phylogenetic reconstruction (using the plastid regions rps16 and trnL-F, and the nuclear ITS and ETS), aiming to answer the following questions: is it a hybrid?; is it an autopolyploid of C. spiralis?; or, if it is a different species, is it even phylogenetically related to C. spiralis or C. arabicus? The studies performed did not indicate any evidence of polyploidy, however, a chromosomal polymorphism was observed between the populations of the taxon studied. The phylogenetic position of this peculiar taxon with C. erythrophyllus, C. spiralis, and C. varzearum also excludes the putative partial heritage of C. arabicus which had been previously hypothesized. Our results confirm that it is a new, undescribed species, which is confirmed by our morphological observations of floral features. A complete taxonomic treatment of the new species is provided, including a key for the species of the genus in the Atlantic Forest. [ABSTRACT FROM AUTHOR]

• Two high quality Cyanobacteria MAGs were recovered from a freshwater lake, Brazil. • The MAGs were identified as Raphidiopsis (= Cylindrospermopsis) raciborskii. • The new MAGs increased the pangenome size by 11 % improving the core/pangenome ratio. • Pangenome-based phylogeny confirmed SouthAmerican (SA) strains' closer relationship. • The SA clade distinctness, with unique saxitoxin producing ability, was reinforced. Two Raphidiopsis (= Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation. [ABSTRACT FROM AUTHOR]

Background: Biribá ( Annona mucosa Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100-4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2 n = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of A. mucosa , we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication., Methodology: We performed chromosome counts of A. mucosa from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus Annona and for A. mucosa ., Results: We observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of A. mucosa is inferred to be polyploid and diverged before domestication., Conclusions: We conclude that, when domesticated, A. mucosa was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in Annona mucosa ., Competing Interests: The authors declare that they have no competing interests., (© 2023 Serbin et al.)

Streptococcus agalactiae are important pathogenic bacteria that cause severe infections in humans, especially neonates. The mechanism by which ST-17 causes invasive infections than other STs is not well understood. In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated in Brazil using the Illumina HiSeq 2500 technology. S. agalactiae GBS90356 ST-17 belongs to the capsular type III and was isolated from a neonatal with a fatal case of meningitis. The genome presented a size of 2.03 Mbp and a G + C content of 35.2%. S. agalactiae has 706 genes in its core genome and an open pan-genome with a size of 5.020 genes, suggesting a high genomic plasticity. GIPSy software was used to identify 10 Pathogenicity islands (PAIs) which corresponded to 15% of the genome size. IslandViewer4 corroborated the prediction of six PAIs. The pathogenicity islands showed important virulence factors genes for S. agalactiae e.g. neu, cps, dlt , fbs , cfb, lmb. SignalP detected 20 proteins with signal peptides among the 352 proteins found in PAIs, which 60% were located in the SagPAI_5. SagPAI_2 and 5 were mainly detected in ST-17 strains studied. Moreover, we identified 51 unique genes, 9 recombination regions and a large number of SNPs with an average of 760.3 polymorphisms, which can be related with high genomic plasticity and virulence during host-pathogen interactions. Our results showed implications for pathogenesis, evolution, concept of species and in silico analysis value to understand the epidemiology and genome plasticity of S. agalactiae. • The first genome S. agalactiae ST-17 strain isolated in Brazil was sequenced (2.03 Mbp). • Pan-genome of S. agalactiae GBS90356 strain exhibited high plasticity. • GIPSy identified 10 pathogenicity islands and IslandViewer4 predicted 6. • Pathogenicity islands associated with integrases were found mainly in S. agalactiae ST-17. [ABSTRACT FROM AUTHOR]

Objectives: Klebsiella pneumoniae sequence type 307 (ST307) has emerged as a new high-risk clone worldwide. The aim of this study was to report the draft genome sequence of a multidrug-resistant CTX-M-15-positive K. pneumoniae strain causing urinary tract infection in a companion animal in Brazil., Methods: Whole-genome sequencing was performed on an Illumina NextSeq platform and the genome was de novo assembled using SPAdes. Data analysis was performed using online tools from the Center for Genomic Epidemiology., Results: The genome size of K. pneumoniae strain PRETA was calculated at 5 450 575 bp, containing a total of 5355 protein-coding sequences. The strain was assigned to the high-risk ST307 and carried the clinically relevant bla CTX-M-15 gene, besides other genes conferring resistance to aminoglycosides, tetracyclines, quinolones, trimethoprim and fosfomycin., Conclusion: These data offer novel information for comparative genomic analyses in order to track the transmission dynamics and epidemiology of the newly emerging high-risk clone ST307., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

A canine parvovirus (CPV)-like virus was detected by PCR and isolated from dead coatis in Argentina. Analysis of the full-length genome sequence revealed that it resembled CPV-but also contained a mutation in the VP2 protein (Arg377Ser) that has not been described previously. This is the first report of a CPV-like virus producing clinical disease in coatis. Genetic similarity to CPV-2c viruses detected in Brazil suggests a strong relationship between these viruses. Although the pathogenic potential of CPV- and feline panleukopenia virus (FPV)-like strains in wild animals is still not completely understood, this study highlights the importance of parvoviruses as a threat to wildlife if proper conditions are present.

In Brazil, A. baumannii has been described as nosocomial pathogens causing hospital-acquired infections. Current WGS technologies have been useful in identifying of genetic features between Acinetobacter isolates. Here, we report the draft genome sequence of OXA-23 producing A. baumannii CCBH15815 clinical isolate, belonging to ST730/ST783, recovered from a 21-year-old hospitalised patient. We observed important resistance determinant genes, especially beta-lactamases-encoding genes, in an estimated genome size of 4,058,633 bp with 3839 predicted coding regions.

Objectives: Genomic surveillance studies monitoring the dissemination of multidrug-resistant Enterobacteriaceae in polluted aquatic ecosystems are urgently required. The aim of this study was to report the draft genome sequence of an MCR-1 and CTX-M-8 co-producing Escherichia coli isolated from a polluted mangrove ecosystem in Northeast Brazil., Methods: Total genomic DNA was sequenced on an Illumina NextSeq platform and was assembled using CLC Genomics Workbench. The whole-genome sequence was evaluated through bioinformatics tools available from the Center of Genomic Epidemiology as well as additional in silico analysis., Results: The genome size was calculated at 5089467bp, comprising a total of 5068 protein-coding sequences. The strain was assigned to sequence type 58 (ST58) and revealed the presence of mcr-1, bla CTX-M-8 and other clinically significant genes responsible for conferring resistance to colistin, β-lactams, trimethoprim and quinolones. In addition, genes conferring resistance to silver (silR) and quaternary ammonium compounds (sugE) were identified., Conclusion: These data provide valuable information for comparative genomic analysis regarding the dissemination of MCR-1-producing E. coli at the human-animal-environment interface., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

In this work, we report the complete genome sequence of, production of polyclonal antibodies against, and development of biological assays for a putative new potexvirus, named senna mosaic virus (SenMV), found infecting Senna occidentalis in the state of São Paulo, Brazil. The complete genome sequence of SenMV comprises 6775 nucleotides excluding the poly(A) tail. The genome organization is similar to those of other potexviruses, with five open reading frames coding for RNA-dependent RNA polymerase (RdRp), the triple gene block (TGB 1, 2, and 3) proteins, and coat protein (CP). The virus was transmitted to S. occidentalis by mechanical inoculation and trimming scissors, but not by seeds.

The Brazilian Amazon Region is a highly endemic area for hepatitis B virus (HBV). However, little is known regarding the genetic variability of the strains circulating in this geographical region. Here, we describe the first full-length genomes of HBV isolated in the Brazilian Amazon Region; these genomes are also the first complete HBV subgenotype D3 genomes reported for Brazil. The genomes of the five Brazilian isolates were all 3,182 base pairs in length and the isolates were classified as belonging to subgenotype D3, subtypes ayw2 (n = 3) and ayw3 (n = 2). Phylogenetic analysis suggested that the Brazilian sequences are not likely to be closely related to European D3 sequences. Such results will contribute to further epidemiological and evolutionary studies of HBV.

The high occurrence of nosocomial multidrug-resistant (MDR) microorganisms is considered a global health problem. Here, we report the draft genome sequence of a MDR Pseudomonas aeruginosa strain isolated in Brazil that belongs to the endemic clone ST277. The genome encodes important resistance determinant genes and consists of 6.7 Mb with a G+C content of 66.86% and 6,347 predicted coding regions including 60 RNAs.