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Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

Anthracnose is becoming one of the main threats to soybean production and is considered the most important disease in some soybean-producing areas. Colletotrichum truncatum is the species most commonly associated with anthracnose and produces microsclerotia. The role of these structures in the epidemiology of soybean anthracnose disease has not yet been described. This study intended to determine if C. truncatum microsclerotia can survive and maintain pathogenicity for periods of up to 246 days, corresponding to the off-season period of soybean in Brazil. Therefore, microsclerotia of two pathogenic isolates of C. truncatum (CMES1059 and LFN0297) were produced and placed in polyester bags, which were kept under field conditions either on the soil surface under maize straw or buried 8 cm deep. The bags were collected monthly for periods of up to 246 days to assess the viability of microsclerotia using germination and typical colony growth. The logistic regression model was used for data analyses considering viable and non-viable microsclerotia. In addition, periodic sowings of soybean were made in soil infested with LFN0297 microsclerotia to test pathogenicity up to 246 days after soil infestation. Colletotrichum truncatum microsclerotia survived from 92 to 246 days in the field soil, with the highest recovery of viable microsclerotia at 153 days. Colletotrichum truncatum was reisolated from soybean plants sown in infested soil 245 days post-inoculation. The isolates from the last microsclerotia sampling from the field (246 days) and those obtained from a plant at the last sowing date (245 days) had the same genotypic profile for 12 microsatellite loci as the isolates used to perform the experiments. Colletotrichum truncatum microsclerotia in soil may serve as the primary inoculum source of soybean anthracnose.

Invasions by fungal plant pathogens pose a significant threat to the health of agriculture ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses in crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen on soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2 to 30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss “The Means, Motive, and Opportunity” of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographic areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.

Citrus post-bloom fruit drop (PFD) is caused by Colletotrichum acutatum and C. gloeosporioides species complexes and frequently occurs in Sao Paulo (SP) state, Brazil. The environmental requirements for conidial germination and appressorium formation have been already determined in vitro; however, the environmental conditions for infection in citrus flowers remain unknown. C. acutatum is considered the main species complex causing PFD in citrus, but a survey of the pathogen’s prevalence has never been performed in SP state. The aims of this study were to assess the influence of different temperatures and wetness periods on infection of flowers by C. acutatum and C. gloeosporioides in potted citrus trees, and to determine the prevalence of both pathogens in different SP regions and sweet orange varieties. Environmental requirement trials were conducted in 2- to 3-year-old potted sweet orange trees. Flowers at different development stages (R2, R4 and R5) were inoculated with C. acutatum and C. gloeosporioides, and the trees were incubated at 18 or 24 °C for wetness periods of 6, 8, 12, 16 or 24 h. The percentages of inoculated flowers with PFD lesions and persistent calyces were calculated. The prevalence of both pathogens in SP regions was assessed in samples of diseased flowers collected at 16 commercial orchards of ‘Natal’, ‘Valencia’ and ‘Pera’ sweet oranges. The species complex was confirmed by isolation and PCR with species complex-specific primers. Blossom blight and persistent calyx incidences were higher in flowers inoculated with C. acutatum than in those inoculated with C. gloeosporioides. Incubation periods ranged from 2 to 5 days, and from 5 to 6 days for C. acutatum and C. gloeosporioides, respectively. In SP, irrespective of the region and sweet orange variety, C. acutatum was isolated from more than 80% of symptomatic flowers. We concluded that C. acutatum is not only more aggressive than C. gloeosporioides for causing PFD but also more prevalent in SP orchards.

Downy mildew, caused by Plasmopara viticola, is the main disease affecting vineyards in subtropical Brazil. Here, we collected 94 P. viticola isolates from four organic and conventional vineyards in the two main grape-growing states of Brazil to evaluate the sensitivity to the quinone outside inhibitor (QoI) azoxystrobin by pheno- and genotyping assays. The impact of location, production system and sensitivity to QoI fungicides on the population genetics and structure of P. viticola was determined using 10 microsatellite markers. Cytochrome b sequencing revealed that 28 and 100% of the isolates from vineyards under organic and conventional management carried the G143A mutation, respectively. The G143A mutation was associated with high levels of azoxystrobin resistance. Three out of the 94 isolates analyzed carried the M125I alteration, not previously described in P. viticola, which was associated with a five-fold reduction in azoxystrobin sensitivity compared to wild-type isolates. Haplotype network analysis based on cytochrome b gene sequences suggested that the Brazilian populations are more closely related to the European than the North American population. A total of six haplotypes were identified, with two of them carrying the G143A mutation. Microsatellite analysis revealed high allelic and genotypic variation among the four populations. Population differentiation analyses indicated that state of origin directly influences the population biology of P. viticola, while production system and QoI sensitivity have little effect. Great genetic diversity, sexual reproduction and high levels of admixture were observed in Rio Grande do Sul State. In contrast, populations in Sao Paulo State were dominated by a few clonal genotypes, and no admixed genotype was detected between the two genetic pools identified in the state. This study raises the hypothesis that winter weather conditions and vine pruning management influence the overwinter survival strategy with profound effects in the population biology of P. viticola.

Colletotrichum is a large genus of plant pathogenic fungi comprising more than 200 species. In this work, we present the genome sequences of four Colletotrichum species pathogenic to soybean: C. truncatum, C. plurivorum, C. musicola, and C. sojae. While C. truncatum is globally considered the most important pathogen, the other three species have been described and associated with soybean only recently. The genome sequences will provide insights into factors that contribute to pathogenicity toward soybean and will be useful for further research into the evolution of Colletotrichum.

Soybean (Glycine max L.) is one of the most important crops worldwide as a source of protein-rich foods and animal feeds. Anthracnose, one of the major limiting factors to soybean production (Dias et al. 2016), is caused by species such as Colletotrichum truncatum, C. sojae, and C. plurivorum (Damm et al. 2009, 2019). In December 2016 and 2017, soybean plants of cultivars Monsoy 8768 and Pioneer y-70 with typical symptoms of anthracnose (necrotic and irregular brown lesions on stems, leaves, and pods) were collected in Mato Grosso, Brazil. Commercial fields sampled showed 10 to 15% incidence of anthracnose in 1 ha in each sampled area. In total, 10 different geographic locations were sampled. Colletotrichum strains were isolated and cultured on potato dextrose agar at 25°C with a 12-h light photoperiod from surface-disinfected (70% alcohol followed by 0.5% sodium hypochlorite) plant tissues. Among others, three single-spore isolates (LFN0048 from Sinop, LFN0074 and LFN0090 from Lucas do Rio Verde) showed different morphology; isolates LFN0048 and LFN0074 were selected for further characterization. Total DNA was extracted and partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), and β-tubulin (TUB2) genes were amplified and sequenced. The sequences were deposited in GenBank (accession numbers MN604249 and MK163893 for HIS3, MN604248 and MK142674 for GAPDH, and MN604250 and MK142675 for TUB) and were compared with most similar reference sequences of Colletotrichum (Damm et al. 2019). Both isolates clustered with Colletotrichum musicola epitype (CBS 132885), showing 100 and 98.5% similarity in GAPDH, 99.5 and 98.9% in HIS3, and 99.2% in TUB2. On PDA, colonies showed dark-gray aerial mycelium with entire margins, reverse violaceous-black. Conidia and ascospore size and shape match those previously described by Damm et al. (2019): 12.12 to 15.86 × 4.93 to 6.95 µm and 15.5 to 19.34 × 5 to 7.84 µm, respectively (n = 100). Appressoria (n = 50) were single or in loose groups, violaceous-black with predominant obovoid, truncated, and cylindrical shapes, with smooth, undulate, or lobate margin, and 9.25 to 29.79 × 7.22 to 21.06 µm. Perithecia, paraphyses; and unitunicate eight-spored asci were also observed. Asci were cylindrical to clavate, smooth-walled, and 48.12 to 68.78 × 9.59 to 14.47 µm (n = 50). Soybean anthracnose is seed-borne (Dias et al. 2018; Rogério et al. 2017); therefore, pathogenicity tests were carried out on pregerminated seeds. Five seeds of Brasmax 8579 cultivar were inoculated with 10 µl of a conidial suspension (106 conidia/ml) that was placed in the emerging radicle, and five mock-inoculated seeds were used as a control. Seedlings were planted in vermiculite and incubated at 25°C with a 12-h photoperiod. After 7 days, inoculated plants showed necrotic lesions on the cotyledons, leaflets, and hypocotyl, whereas control plants remained asymptomatic. The experiment was repeated three times. C. musicola was reisolated from the symptomatic tissues, and the identity was confirmed by morphology and multilocus phylogeny. Until now, C. musicola has been reported to be associated with Musa sp. (Damm et al. 2019) and Colocasia esculenta (Vásquez-López et al. 2019) in Mexico, and with Phaseolus lunatus in Brazil (Cavalcante et al. 2018). To our knowledge, this is the first report of C. musicola joining a group of new and emergent species of Colletotrichum causing anthracnose in soybean-producing regions around the world.

Aims Fungal diseases are among the main factors limiting high yields of soybean crop. Colletotrichum isolates from soybean plants with anthracnose symptoms were studied from different regions and time periods in Brazil using molecular, morphological and pathogenic analyses. Methods and Results Bayesian phylogenetic inference of GAPDH, HIS3 and ITS-5.8S rDNA sequences, the morphologies of colony and conidia and inoculation tests on seeds and seedlings were performed. All isolates were clustered only with Colletotrichum truncatum species in three well-separated clusters. Intraspecific genetic diversity revealed 27 distinct haplotypes in 51 fungal isolates; some of which were identical to C. truncatum sequences from other regions around the world, while others were related to alternative hosts. Conidia were falcate, hyaline, unicellular and aseptate, with variable dimensions, formed in acervuli. Despite being pathogenic to seedlings by both inoculation methods, variation was observed in the aggressiveness of the tested isolates, which was not correlated to genetic variation. Conclusion The identification of C. truncatum in the sampled isolates evidenced it being the only causal agent of soybean anthracnose in Brazil until 2007, with relevant genetic, morphological and pathogenic variability as well as a broad geographical origin. The wide distribution of the predominant C. truncatum haplotype indicated the existence of a highly efficient mechanism of pathogen dispersal over long distances, reinforcing the role of seeds as the primary source of disease inoculum. Significance and Impact of the Study The characterization and distribution of Colletotrichum species in soybean-producing regions in Brazil is fundamental for understanding the disease epidemiology and for ensuring effective control strategies against anthracnose. This article is protected by copyright. All rights reserved.

Postbloom fruit drop is an important citrus disease caused by Colletotrichum acutatum. Severe outbreaks can develop when rainy periods occur during citrus bloom. Under these conditions, explosive epidemics are observed despite relatively short inoculum dispersal distances typical of this pathogen. C. acutatum can survive on citrus leaf surfaces after formation of appressoria, but survival on weeds has not been characterized. The survival of C. acutatum on seven species of weeds was evaluated under greenhouse conditions by artificial inoculation and subsequent recovery of the pathogen in-vitro. Conidial germination and appressorial development of C. acutatum were observed on the surface of all inoculated leaves. The pathogen was recovered from weed leaves at 30, 60 and 90 days after inoculation. Statistically, there was no difference in survival of C. acutatum among sample times post-inoculation. Although survival varied on different weed species, no symptoms were observed on inoculated leaves. All citrus flowers inoculated with isolates recovered from inoculated weeds showed typical symptoms of postbloom fruit drop. We conclude that the weed species tested may serve as potential alternative hosts for C. acutatum.

BGPI : équipe 5; International audience; Knowledge of the population structure, genetic diversity, and reproductive mode of plant pathogens can help to implement effective disease management strategies. Anthracnose is one of the most prominent diseases in soybean and is mainly associated with the species Colletotrichum truncatum. However, the genetic structure of C. truncatum populations associated with soybean remains unknown. We collected C. truncatum isolates from 10 sites representing two Brazilian states (Mato Grosso and Goiás) and used 13 highly polymorphic microsatellite markers to investigate the population genetic structure of the pathogen. Analyses revealed high gene and haplotypic diversity within populations, as well low genetic differentiation and sharing of multilocus haplotypes among populations and regions. Bayesian and multivariate analysis revealed the presence of three distinct genetic clusters with at least two coexisting in all locations, and all of them coexisting in eight locations. We found limited evidence for admixture between clusters, with only two isolates showing nonzero membership with a second cluster. Analyses of linkage disequilibrium rejected the hypothesis of random mating in all clusters, but values of the index of association were low and not consistent with long-term lack of sexual reproduction. Our findings suggest that Brazilian C. truncatum populations resulted from at least three founder events that led to three genetic clusters that spread throughout the country, raising questions with respect to the factors allowing their maintenance in syntopy without evidence of admixture between them.

Background Giardia duodenalis (synonyms G. lamblia and G. intestinalis) is an enteric protozoan parasite of a wide range of mammalian hosts, including humans and various domestic and wild animals. There is considerable genetic variability in G. duodenalis and isolates of this parasite have been divided into eight genetic assemblages. Microsatellites markers can be used to discriminate isolates with a high level of sensitivity. This study was conducted to identify and characterize genomic microsatellites (simple sequence repeats—SSRs), sequences of one- to six-nucleotide motifs repeated in tandem, present in the available genomes of G. duodenalis and to develop new markers that can serve as a tool for detection and for characterizing the genetic diversity of this parasite. Methodology/ Principal findings For each genetic assemblage, polymorphism levels for the microsatellite markers were evaluated. After performing the analysis using the MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified. In all the genomes, trinucleotide repeats were the most common class followed by tetranucleotide. Many of the SSR loci are assemblage-specific, and 36 SSR loci shared among all the genomes were identified. Together with hypothetical proteins, variant-specific surface proteins represented nearly half of the annotated SSR loci. The results regarding the most common repeat among the SSRs led us to infer that positive selection occurred to avoid frameshift mutations. Additionally, based on inter- and intra-genetic assemblages polymorphism analyses, we unveiled previously undetected genetic variation, indicating that the microsatellite markers we developed are useful molecular tools for epidemiological inferences based on population genetics patterns and processes. Conclusions There is increasing demand for the development of new molecular markers and for the characterization of pathogens at a higher resolution level. In this study, we present 60 G. duodenalis microsatellites markers that exhibited high polymerase chain reaction (PCR) amplification efficiency among the different genetic assemblages. Twenty of these markers presented nucleotide sequence polymorphisms and may be used as a genotyping tool. The monomorphic markers can be used for the detection of the parasite at the species and genetic assemblage level. These polymorphic markers revealed a genetic diversity that was previously undetectable, thus they can be considered valuable molecular tools for high resolution markers in future studies investigating Giardia and may also be used for epidemiological inferences based on populations genetics patterns and processes., Author summary Giardia duodenalis is a protozoan parasite that causes giardiasis, a disease that affects millions of people worldwide and a wide range of mammalian hosts. G. duodenalis presents considerable genetic variability and there is an increasing demand for the development of new molecular markers. This study aimed to identify and characterize genomic microsatellites of Giardia based on the different available genomes. After performing an analysis using MISA and SciRoKo software, 1,853 simple sequence repeats (SSRs) were identified and many of them were annotated as variant-specific surface proteins. We detected 20 polymorphic SSRs, including one shared among all available genomes. Because the markers are based on a simple PCR, they have a great potential for use in future studies of Giardia through PCR, genetic sequencing or genotyping by real-time PCR.

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

Rhizophora mangle L. (Rhizophoraceae) grows on aerial roots, which emerge above the water level, giving stands of this tree the characteristic “mangrove” appearance. To produce in situ and ex situ information for genetic conservation programs for this species, we investigated the genetic diversity and mating system of one R. mangle population. We sampled 30 adult trees and a total of 349 seeds in Northern Brazil. We genotyped all adult trees and seeds with four microsatellite loci. The average fixation index was -0.222 for adult trees and 0.030 for seeds. The multilocus outcrossing rate (t m =0.921) was significantly lower than unity (1.0). There was no substantial evidence of null alleles nor genotypic disequilibrium among the loci. The combined power to exclude the first parent probability was 0.921. The average coancestry coefficient (=0.180) was similar to that expected for half-sib progenies (=0.125). Thus, the number of adult trees necessary for seed collection to obtain progeny arrays with an effective size of 150 was estimated to be 62. In conclusion, this study produced important information for the management and conservation of R. mangle and will contribute to conservation and management programs for this species.

Anthracnose is an important disease in vineyards in South and Southeast Brazil, the main grape-producing regions in the country. This study aimed to identify the causal agents of grapevine anthracnose in Brazil through multilocus phylogenetic analyses, morphological characterization and pathogenicity tests. Thirty-nine Elsinoe ampelina and 13 Colletotrichum spp. isolates were obtained from leaves, stems and berries with anthracnose symptoms collected in 38 vineyards in southern and southeastern Brazil. For E. ampelina isolates, the internal transcribed spacer (ITS), histone H3 (HIS3) and elongation factor 1-α (TEF) sequences were analysed. HIS3 was the most informative region with 55 polymorphic sites including deletions and substitutions of bases, enabling the grouping of isolates into five haplotypes. Colonies of E. ampelina showed slow growth, variable colouration and a wrinkled texture on PDA medium. Conidia were cylindrical to oblong with rounded ends, hyaline, aseptate, (3.57-) 5.64 (-6.95) μm long and (2.03-) 2.65 (-3.40) μm wide. Seven species of Colletotrichum were identified: C. siamense, C. gloeosporioides, C. fructicola, C. viniferum, C. nymphaeae, C. truncatum and C. cliviae, with a wide variation in colony and conidium morphology. Only E. ampelina caused anthracnose symptoms on leaves, tendrils and stems in Vitis vinifera and V. labrusca. High disease severity and a negative correlation between disease severity and shoot dry weight were observed only when relative humidity was above 95%. In this study, only E. ampelina caused anthracnose symptoms on grapevine shoots in Brazil. This article is protected by copyright. All rights reserved.

We assessed the pollen and seed dispersal patterns, genetic diversity, inbreeding and spatial genetic structure of Himatanthus drasticus (Apocynaceae), a tree native to the Brazilian Savanna (Cerrado) that is heavily exploited for its medicinal latex. The study was conducted in the Araripe National Forest, Ceara State, Brazil. Within a one-hectare plot, samples were collected from all adult trees, adult trees located in the immediate vicinity of the plot, and seedlings. All sampled individuals were mapped and genotyped using microsatellite markers. High levels of polymorphism and significant levels of inbreeding were found, which indicates that self-fertilisation and mating among relatives occur in this population. Both the adults and seedlings had significant spatial genetic structure up to ~40 m and our results confirmed the occurrence of isolation by distance. Pollen and seeds were dispersed over short distances and immigration of pollen and seeds into the plot was estimated at 13 and 9 %, respectively. Taking into consideration the degree of inbreeding, relatedness, intrapopulation spatial genetic structure and pollen dispersal distance, we recommend collecting seeds from a large number of trees spaced at least 150 m apart to avoid collecting seeds from related individuals and an overlap of pollen pools among seed trees.

The importance of genetic variation for maintaining biological diversity and evolutionary processes is widely accepted; however, limited action has been taken to protect genetic diversity in natural populations. Until recently, it was assumed that the exploitation of non-timber forest products, such as fruits, barks and exudates, had low environmental impact, but recognition that the harvesting of these plants can affect several biological levels, including genetic diversity and structure, has been growing. Nevertheless, the effect of harvesting non-timber forest products on the genetic diversity of the harvested species is poorly understood. The objective of this work is to assess the impact of harvesting on the genetic diversity of Himatanthus drasticus (Apocynaceae), a tree of the Brazilian Savanna (Cerrado) that is highly exploited for its medicinal latex. We tested the hypothesis that harvesting can cause a trade-off between survival and reproduction in H. drasticus, reducing the effective population size as well as the genetic diversity in highly exploited populations. The study was conducted in the Araripe National Forest, a preserved Cerrado area in Ceara State, Brazil. We sampled six populations that included two different levels of harvesting (high-harvest and low-harvest) and characterized the genetic diversity and structure in two groups (adults and seedlings) using microsatellite markers. We verified high levels of polymorphism in H. drasticus; however, significant levels of inbreeding in all studied populations were also observed. We found a higher degree of genetic structure in the seedling group when compared with the adult group, a difference that was most likely due to seed rain deposited in nearby locations. No differences were detected in adult genetic diversity levels between populations under different harvesting intensities. However, seedling allelic richness was significantly lower in the high-harvested populations, indicating allelic losses that may be associated with the exploitation of bark and latex. Evidence of genetic loss due to overharvesting was supported by significant bottleneck signatures observed in the seedling group of two out of three high-harvest populations. The establishment of a conservation strategy is imperative to avoid future genetic losses and ensure the long-term viability of H. drasticus populations. The information obtained in this study has been integrated with ecological information about the effects of latex tapping on phenology, demography and biomass recovery of exploited populations, with the goal of proposing a sustainable management plan for the species.

Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in various hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas. The results showed high diversity of haplotypes and substantial genetic similarity between clinical and environmental groups of G. duodenalis. We demonstrated sharing of Giardia genotypes among the different populations studied. The comparison between veterinary and human sequences led us to identify new zoonotic genotypes, including human isolates from genetic assemblage C. The application of a population genetic analysis in epidemiological studies allows quantification of the degree of genetic similarity among populations of Giardia duodenalis from different sources of contamination. The genetic similarity of Giardia isolates among human, veterinary, and environmental groups reinforced the correlation between clinical and environmental isolates in this region, which is of great importance for public health.

Citrus crops in São Paulo State, Brazil, have been severely affected by postbloom fruit drop disease (PFD), which is caused by Colletotrichum acutatum. This disease leads to the drop of up to 100% of young fruits. Previous studies have assumed that this pathogen exhibits a clonal reproductive mode, although no population genetic studies have been conducted so far. Thus, the genetic structure of six C. acutatum populations from sweet orange orchards showing PFD symptoms was determined using nine microsatellite markers, enabling inference on predominant mode of reproduction. C. acutatum populations exhibit a nearly panmictic genetic structure and a high degree of admixture, indicating either ongoing contemporary gene flow at a regional scale or a recent introduction from a common source, since this pathogen was introduced in Brazil only very recently. Sharing haplotypes among orchards separated by 400 km suggests the natural dispersal of fungal propagules, with the possible involvement of pollinators. A significant population expansion was detected, which was consistent with an increase in host density associated with crop expansion toward new areas across the state. Findings of moderate to high levels of haplotypic diversity and gametic equilibrium suggest that recombination might play an important role in these pathogen populations, possibly via parasexual reproduction or a cryptic sexual cycle. This study provides additional tools for epidemiological studies of C. acutatum to improve prevention and management strategies for this disease.

Premise of the study: Bathysa australis is a common subcanopy tree from the Atlantic Forest that is pollinated by bees and wasps and produces autochoric seeds. This species exhibits great phenotypic plasticity along the elevational gradient of Serra do Mar in southeastern Brazil. We expect to assess the genetic diversity and gene flow between populations of this species along the elevational gradient. Methods and Results: We developed a microsatellite-enriched genomic library for B. australis, and 10 microsatellite loci were successfully amplified, ranging from one to 13 alleles per locus. The observed and expected heterozygosities ranged from 0.333 to 0.900 (average: 0.629) and 0.564 to 0.900 (average: 0.742), respectively. Conclusions: These are the first microsatellite markers developed for the genus Bathysa and may be useful in other species of the Condamineeae tribe. These primers will be an important tool for studies of population ecology and conservation genetics.