Characterization Of Genetic Diversity Research Articles

The tree that hides the forest: cryptic diversity and phylogenetic relationships in the Palaearctic vector Obsoletus/Scoticus Complex (Diptera: Ceratopogonidae) at the European level

BackgroundCulicoides obsoletus is an abundant and widely distributed Holarctic biting midge species, involved in the transmission of bluetongue virus (BTV) and Schmallenberg virus (SBV) to wild and domestic ruminants. Females of this vector species are often reported jointly with two morphologically very close species, C. scoticus and C. montanus, forming the Obsoletus/Scoticus Complex. Recently, cryptic diversity within C. obsoletus was reported in geographically distant sites. Clear delineation of species and characterization of genetic variability is mandatory to revise their taxonomic status and assess the vector role of each taxonomic entity. Our objectives were to characterize and map the cryptic diversity within the Obsoletus/Scoticus Complex.MethodsPortion of the cox1 mitochondrial gene of 3763 individuals belonging to the Obsoletus/Scoticus Complex was sequenced. Populations from 20 countries along a Palaearctic Mediterranean transect covering Scandinavia to Canary islands (North to South) and Canary islands to Turkey (West to East) were included. Genetic diversity based on cox1 barcoding was supported by 16S rDNA mitochondrial gene sequences and a gene coding for ribosomal 28S rDNA. Species delimitation using a multi-marker methodology was used to revise the current taxonomic scheme of the Obsoletus/Scoticus Complex.ResultsOur analysis showed the existence of three phylogenetic clades (C. obsoletus clade O2, C. obsoletus clade dark and one not yet named and identified) within C. obsoletus. These analyses also revealed two intra-specific clades within C. scoticus and raised questions about the taxonomic status of C. montanus.ConclusionsTo our knowledge, our study provides the first genetic characterization of the Obsoletus/Scoticus Complex on a large geographical scale and allows a revision of the current taxonomic classification for an important group of vector species of livestock viruses in the Palaearctic region.

The correlation between total immunoglobulin-E levels and interleukin-13 gene polymorphism in asthmatic children treated with inhaled corticosteroids or montelukast

Background: The aim of this research was to study the possible correlation between single-nucleotide polymorphism of interleukin (IL)-13-1112 C/T with specific parameters in asthmatic children (total serum immunoglobulin-E [TSIgE] levels and asthma severity) treated with montelukast or inhaled corticosteroid. Methods: The study included one hundred asthmatic patients attending Karbala Teaching Hospital for children and similar numbers of healthy unrelated age-matched controls from the same locality of Iraq. TSIgE levels were determined by ELISA technique. DNA was extracted and processed by the allele-specific polymerase chain reaction technique for characterization of genetic variants of IL-13-1112 C/T gene polymorphisms. Results: Iraqi children with asthma showed a lower frequency of the IL-13-1112 CC genotype (13% vs. 16%) for control cases with a higher frequency of the heterozygous IL-13-1112 CT genotype (78% vs. 75%). IL-13-1112 showed significantly negative association with asthma in the dominant, codominant, and overdominant models of inheritance. On the other hand, comparing genotypes of subgroups related to gender, asthma severity, and asthma control showed a nonsignificant difference (P > 0.05). Homozygous wild types of IL-13-1112 TT might be considered protective to Iraqi asthma children. Conclusion: The IL-13 gene may be associated with the level of control in treated asthmatic patients. There is no correlation between TSIgE and the SNP.

Association mapping for grain diameter and weight in lentil using SSR markers

The grain diameter and weight are important traits in lentil influencing grain yield, cooking time and consumer preference. In this study association mapping panel of ninety-six diverse genotypes representing genotypes from India and Mediterranean region was assessed at three locations in India (Delhi, Indore, and Dharwad representing different cultivation zones) for grain size and weight. Hundred grain weight ranged from 1.24 to 5.8 g across the locations and grain diameter from 1.91 mm to 5.98 mm. Marker-trait associations (MTAs) were analysed with 425 markers (365 EST-SSRs and 60 genomic markers) using mixed linear model (MLM). The characterization of genetic variation using STRUCTURE analysis revealed the presence of six sub-populations. Neighbor-Joining method of clustering also confirmed six clusters. The MLM approach identified association of PBALC 224 (R2 value 7%) with grain diameter and GLLC 614 (R2 value of 13%) and PBALC 29 (R2 value of 15%) with grain weight. The reported SSRs exhibited the marker-trait association across the all studied environments. The identified SSRs exhibited consistent performance across three locations. This study can help in breeding new lines with enhanced grain diameter and weight using marker-assisted selection (MAS) in lentil.

Characterization of LDLR rs5925 and PCSK9 rs505151 genetic variants frequencies in healthy subjects from northern Chile: Influence on plasma lipid levels.

BackgroundIdentification and characterization of genetic variants and their effects on human health may allow to establish relationships between genetic background and susceptibility to developing cardiovascular diseases. LDLR and PCSK9 polymorphisms have been associated with higher lipid levels and risk of cardiovascular diseases. Thus, the main aim of this study was to evaluate genotype distribution and relative allelic frequency of LDLR rs5925 (1959C > T) and PCSK9 rs505151 (23968 A > G) genetic variants and their effects on lipid levels of healthy subjects from northern Chile.MethodsA total of 178 healthy individuals were recruited for this study. The genotyping of rs5925 (LDLR) and rs505151 (PCSK9) polymorphisms was performed by PCR‐RFLP and qPCR, respectively. In addition, glucose and lipid levels were determined and associated with the genetic data.ResultsGenotype distribution for LDLR rs5925 polymorphism was as follows: CC = 19%; CT = 53%; and TT = 28% (HWE: χ 2 = 0.80; P = .37), and for PCSK9 rs505151 genetic variant was as follows: AA = 93%; AG = 7%; and GG = 0% (HWE: χ 2 = 0.22; P = .64). The frequency of T (rs5925) and G (rs505151) mutated alleles was 0.55 and 0.03, respectively. Data showed that individuals carrying LDLR mutated allele (T) presented lower values of total cholesterol, triglycerides, and LDL‐cholesterol when compared to CC homozygous genotype (P < .05). Subgroup analysis revealed that women carrying the PCSK9 mutated allele (G) exhibited higher values of total cholesterol, triglycerides, HDL‐C, and LDL‐C when compared to male group carrying the same genotype (P < .05).ConclusionsThe effect of LDLR rs5925 and PCSK9 rs505151 gene polymorphisms on lipid levels is associated with gender among healthy subjects from northern Chile.

Characterization of Genetic Variation in CYP3A4 on the Metabolism of Cabozantinib in Vitro.

Cabozantinib is a multityrosine kinase inhibitor and has a wide range of applications in the clinic, whose metabolism is predominately dependent on CYP3A4. This study was performed to characterize the enzymatic properties of 29 CYP3A4 alleles toward cabozantinib and the functional changes of five selected alleles (the wild-type, CYP3A4.2.8.14 and .15) toward cabozantinib in the presence of ketoconazole. Cabozantinib, 1-100 μM, with/without the presence of ketoconazole and CYP3A4 enzymes in the incubation system went through 30 min incubation at 37 °C, and the concentrations of cabozantinib N-oxide were quantified by UPLC-MS/MS to calculate the corresponding kinetic parameters of each variant. Collectively, without the presence of ketoconazole, most variants displayed defective enzymatic activities in different degrees, and only CYP3A4.14 and .15 showed significantly augmented enzymatic activities. With the presence of ketoconazole, five tested CYP3A4 alleles, even CYP3A4.14 and .15, exhibited obvious reductions in intrinsic clearance. Besides, we compared cabozantinib with regorafenib in relative clearance to confirm that CYP3A4 has the property of substrate specificity. As the first study of CYP3A4 genetic polymorphisms toward cabozantinib, our observations can provide prediction of an individual's capability in response to cabozantinib and guidance for medication and treatment of cabozantinib.

Long-Read Sequencing Emerging in Medical Genetics.

The wide implementation of next-generation sequencing (NGS) technologies has revolutionized the field of medical genetics. However, the short read lengths of currently used sequencing approaches pose a limitation for the identification of structural variants, sequencing repetitive regions, phasing of alleles and distinguishing highly homologous genomic regions. These limitations may significantly contribute to the diagnostic gap in patients with genetic disorders who have undergone standard NGS, like whole exome or even genome sequencing. Now, the emerging long-read sequencing (LRS) technologies may offer improvements in the characterization of genetic variation and regions that are difficult to assess with the prevailing NGS approaches. LRS has so far mainly been used to investigate genetic disorders with previously known or strongly suspected disease loci. While these targeted approaches already show the potential of LRS, it remains to be seen whether LRS technologies can soon enable true whole genome sequencing routinely. Ultimately, this could allow the de novo assembly of individual whole genomes used as a generic test for genetic disorders. In this article, we summarize the current LRS-based research on human genetic disorders and discuss the potential of these technologies to facilitate the next major advancements in medical genetics.

Aplanar y exhibir la variación: dos estrategias de investigación de la genética humana en México

Introducción: este artículo analiza dos estrategias de investigación puestas en acción en tres proyectos de estudio de la genética humana en México, entre 1960 y 2009. Se distingue entre una estrategia que incorpora recursos multidisciplinarios en el diseño del muestreo, el análisis e interpretación de datos (a la que se le denomina de exhibición), y una que privilegia consideraciones pragmáticas sobre los análisis multidisciplinarios (a la que se le denomina de aplanamiento). Desarrollo: se analizó el trabajo del médico hematólogo Rubén Lisker en la década de 1960, el mapeo de la diversidad genómica mexicana realizado por investigadores del Instituto Nacional de Medicina Genómica entre 2004 y 2009, y el análisis de la variación nativa llevado a cabo por el genetista Andrés Moreno (en la Universidad de Stanford en ese entonces), y sus colegas en años recientes. Conclusiones: las decisiones estratégicas que toman los científicos tienen consecuencias en la medición y caracterización de la variación genética en las poblaciones humanas, pero también sobre las prácticas sociales demográ cas y biomédicas relacionadas con su estudio. Mientras la primera estrategia exhibe de forma detallada la variación genética oculta en las poblaciones humanas, favoreciendo así la precisión y el realismo, la segunda tiende a aplanar las diferencias individuales y a perder profundidad histórica, pero privilegiando la generalización y la descripción de los grandes rasgos de una población.

Pharmacogenetics of Antiretroviral Drug Response and Pharmacokinetic Variations in Indigenous South African Populations.

Interindividual and interethnic differences in response to antiretroviral drugs (ARVs) are influenced by genetic variation. The few genomic studies conducted among African-Americans and African ethnic groups do not reflect the extensive genetic diversity within African populations. ARVs are widely used in Africa. Therefore, genomic characterization of African populations is required before genotype-guided dosing becomes possible. The aim of this study was to determine and report on the frequency of genetic variants in genes implicated in metabolism and transport of ARVs in South African populations. The study comprised 48 self-reported South African Colored (SAC) and 296 self-reported Black African (BA) individuals. Allele and genotype frequency distributions for 93 variants contributing to metabolism and transport of ARVs were compared between groups, and other global populations. Fifty-three variants had significant differences in allele and genotype frequencies when comparing SAC and BA groups. Thirteen of these have strong clinical annotations, affecting efavirenz and tenofovir pharmacokinetics. This study provides a summary of the genetic variation within genes implicated in metabolism and transport of ARVs in indigenous South African populations. The observed differences between indigenous population groups, and between these groups and global populations, demonstrate that data generated from specific African populations cannot be used to infer genetic diversity within other populations on the continent. These results highlight the need for comprehensive characterization of genetic variation within indigenous African populations, and the clinical utility of these variants in ARV dosing for global precision medicine. Population pharmacogenetics is a nascent field of global health and warrants further research and education.

Abstract 229: Genome-wide association study by colorectal carcinoma subtype

Abstract Over 50 genetic variants have been associated with colorectal cancer (CRC) risk through genome-wide association studies (GWAS), yet these variants represent only a fraction of the total estimated heritability. CRC is a heterogenous disease with diverse tumor etiology. Assessing genetic risk in molecular subtypes may help to identify novel loci and characterize genetic risk among tumor subtypes. We used microsatellite instability (MSI), an established CRC classifier with etiological and therapeutic relevance, to define CRC subtypes for GWAS analyses. We conducted a case-case analysis to estimate odds ratios (OR) and 95% confidence intervals (CI) for association of genome-wide variants with microsatellite stable (MSS) versus unstable (MSI) carcinomas. We ran an inverse-variance weighted fixed-effects meta-analysis across GWAS in a discovery set of 4,163 population-based CRC cases with harmonized microsatellite instability (MSI) marker and imputed genotype data. For each analysis, we used log-additive logistic regression, adjusting for age, sex, and principal components to account for population substructure. We then followed up with replication of 102 SNPs that reached p-values less than 5x10-6 in 1,698 cases. A total of 845 (20.3%) cancer cases were microsatellite unstable in the discovery population and 174 (10.2%) were unstable in the replication population. No variants reached the genome-wide significance level of 5x10-8 in the discovery set. However, we identified two variants that reached a Bonferroni corrected p-value of 4.0x10-4 in the replication set. This included one variant in MLH1 (Replication: OR=1.74, 95% CI=1.53-1.98, p=1.63x10-5; Discovery+Replication: OR=1.45, 95% CI=1.37-1.54, p=9.76x10-11) and one variant in LOC105377645 (Replication: OR=1.70, 95% CI=1.49-1.94, p=5.13x10-5; Discovery+Replication: OR=1.45, 95% CI=1.37-1.54, p=9.76 x 10-11). The MLH1 gene is a DNA mismatch repair gene implicated in Lynch Syndrome, the hallmark of which is microsatellite instability. This is the first genome-wide scan to identify a common variant in MLH1 that is associated with CRC. This variant (minor allele frequency, MAF = 23% in this all European ancestry population) is located in the 5'-untranslated region of MLH1 and is thought to act as a long-range regulator of DCLK3, a potential tumor driver gene. The second variant, located in LOC105377645 with an MAF of 22%, is in an uncharacterized region of the genome and has not previously been implicated in cancer development. These findings suggest that accounting for molecular heterogeneity is important for discovery and characterization of genetic variants associated with CRC risk. We plan to run polytomous regression analyses, increase our sample size, and further investigate CRC subtypes by CIMP, BRAF mutation, KRAS mutation status. Citation Format: Tabitha A. Harrison, Yiwen Lu, Chenjie Zeng, Flora Qu, Kristin Anderson, Hermann Brenner, Daniel D. Buchanan, Peter T. Campbell, Andrew T. Chan, Jenny Chang-Claude, Graham G. Giles, Bethany Van Guelpen, Michael Hoffmeister, Mark A. Jenkins, Noralane M. Lindor, Roger L. Milne, Polly A. Newcomb, Reiko Nishihara, Michael O. Woods, Shuji Ogino, John D. Potter, Martha L. Slattery, Wei Sun, Stephen N. Thibodeau, Li Hsu, Ulrike Peters. Genome-wide association study by colorectal carcinoma subtype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 229.

Assessment of genetic diversity in 29 rose germplasms using SCoT marker

Roses are well known for commercial floriculture and greatly used in the field of perfumery, soap, cosmetics, jams & jelly and essential oil production. Due to interspecific hybridization, a large number of hybrids and cultivated varieties of rose are recognized which reveals distinguishable features in flowers such as size, shape, and color. Apart from this, the geographical distribution and polyploidy also make Rose genus more complex. Therefore, the present study was undertaken for the identification and characterization of genetic variation within 29 rose accessions through Start codon targeted polymorphism (SCoT) markers. Out of 36 primers, 32 revealed polymorphic amplification profile in 29 rose accessions with amplification ranging from 150 bp to 1.2 kb. A total of 299 polymorphic amplicons were obtained, ranging from 4 to 19 amplicons with an average of 9.34 amplicons per primer. The polymorphic information content (PIC) ranged from 0.42 to 0.92 with an average of 0.78. The dendrogram was constructed to establish genetic relationship among 29 different accessions using Neighbor-joining and Nei-Li matching coefficient. The distinguishable genetic background and a high degree of variation in the rose genotypes successfully exhibited by the SCoT markers may serve as a valuable aid in Rose improvement strategy.

In vitro, induction of salt tolerant potato (solanum tuberosum l.) Plants with gamma irradiation and characterization of genetic variations through sds-page and issr-pcr analysis

Salt tolerant mutants of potato (Solanum tuberosum L. ‘Sponta’) were obtained via gamma irradiation. bud explants of two strains of potato (Sponta and lady rosetta were treated with various dosages of gamma irradiation, and the clonal generations were developed. Selection of salt-tolerant mutants was accomplished by in vitro selection media containing 30, 60, 90 and 120 mM NaCl. Molecular-level differences between the control and mutant plants were elucidated using ISSR technique, and the polymorphism rate according to the selected primers was calculated as 89.66%. Genetic distances between the controls and mutants were also calculated, and related dendrograms were produced. On average the mutants were genetically 27.5% different from the control plants. The greatest difference encountered between the control and mutants was 47%, which was detected in mutant plants produced by 20 or 30 Gy gamma irradiation and regenerated in selection medium containing 100 mM NaCl.

Genetic variation and population structure of the arboreal bicolored ant Tetraponera rufonigra Jerdon from selected urban locations in eastern Penang Island, Malaysia

Tetraponera rufonigra, commonly known as the arboreal bicolored ant has gained its notoriety as one of the medically-important pest insects in Malaysia. T. rufonigra is recognizable by its excruciating sting, causing a severe anaphylaxis especially to those with the history of allergy. In this study, genetic diversity and population structure of T. rufonigra populations were examined based on a 503 base pair fragment of the mitochondrial DNA Cytochrome Oxidase I (COI) gene. Specimens were collected from six different localities in urban areas in the eastern part of Penang Island. The six populations exhibited high pairwise genetic differentiation (FST), ranging from 0.42 to 1.00 and low gene flow (Nm), ranging from 0.00 to 0.69, except for populations of CSA and CH (FST=0.0, Nm=−1813.68). From AMOVA analysis, a high genetic variation was observed among populations i.e. 99.58% (FST=0.996 p=0.000±0.000). These results provided the basic information for entomologists to better understand the difference of genetic structure of T. rufonigra at a population level and can be further utilized to estimate the contributing factors in the genetic differentiation of this species in urban areas. Our results suggested that the population structure and the gene flow of T. rufonigra in some studied areas might have been affected by the dispersal ability of the insect, environmental conditions, and/or human-mediated dispersal, while, populations of other areas retained their gene flow. These findings might provide useful baseline information for the implementation of area-wide pest management as well as for further characterization of genetic variation and population structure of this medically-important pest.

Adapting plant material to face water stress in vineyards: which physiological targets for an optimal control of plant water status?

&lt;p class="Abstract" style="text-align: justify;"&gt;&lt;strong&gt;Aims:&lt;/strong&gt; Water scarcity, associated with climate change, is a particular threat to the sustainability of viticulture in present areas of cultivation, usually prone to drought. Breeding grapevine for reduced water use, better water extraction and maintained production (i.e., high water use efficiency) is therefore of major interest.&lt;/p&gt;&lt;p class="Abstract" style="text-align: justify;"&gt;&lt;strong&gt;Methods and results:&lt;/strong&gt; This requires a comprehensive knowledge of the physiological impacts of drought on yield and quality. Attention should be paid to those mechanisms involved in the regulation of water status in plant tissues, as it is the primary parameter affected by drought. Transpiration rate, which has a major influence on plant water status, should therefore receive special attention in breeding programs. Beyond scions, the role of rootstocks, which have been largely introduced in vineyards, should be investigated further as it determines water extraction capacity and could modify water balance in grafted plants.&lt;/p&gt;&lt;p class="Abstract" style="text-align: justify;"&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt; Here we review recent advances in the characterization of genetic variability in the control of water use and water status, whether induced by rootstock or scion.&lt;/p&gt;&lt;p class="Abstract" style="text-align: justify;"&gt;&lt;strong&gt;Significance and impact of the study: &lt;/strong&gt;This review should help scientists in choosing the relevant physiological targets in their research on grapevine tolerance to drought, whether for breeding prospects or new management practices.&lt;/p&gt;

Adapting plant material to face water stress in vineyards: which physiological targets for an optimal control of plant water status?

Aims: Water scarcity, associated with climate change, is a particular threat to the sustainability of viticulture in present areas of cultivation, usually prone to drought. Breeding grapevine for reduced water use, better water extraction and maintained production (i.e., high water use efficiency) is therefore of major interest.Methods and results: This requires a comprehensive knowledge of the physiological impacts of drought on yield and quality. Attention should be paid to those mechanisms involved in the regulation of water status in plant tissues, as it is the primary parameter affected by drought. Transpiration rate, which has a major influence on plant water status, should therefore receive special attention in breeding programs. Beyond scions, the role of rootstocks, which have been largely introduced in vineyards, should be investigated further as it determines water extraction capacity and could modify water balance in grafted plants.Conclusion: Here we review recent advances in the characterization of genetic variability in the control of water use and water status, whether induced by rootstock or scion.Significance and impact of the study: This review should help scientists in choosing the relevant physiological targets in their research on grapevine tolerance to drought, whether for breeding prospects or new management practices.

Characterization of genetic variation and basis of inflammatory bowel disease in the Toll-like receptor 5 gene of the red wolf and the maned wolf

Characterization of genetic variation and basis of inflammatory bowel disease in the Toll-like receptor 5 gene of the red wolf and the maned wolf

Molecular Characterization of Genetic Variability among Sudanese Baggara Cattle within Kappa Casein Csn3 Gene (Exon V)

The present work was conducted to detect possible genetic variants of kappa casein (CSN3) gene in Western Baggara cattle in Sudan. This gene is associated with higher fat, protein, and has a significant influence on milk processing properties in comparison to other casein variants. 70 blood samples were collected from Western Baggara cattle in three areas (Hai Elgabal, Bulbul and Umdamm). Genomic DNA was extracted from the whole blood using guanidine chloroform method. A 495 bp fragment containing exon V of kappa casein gene was amplified by PCR using specific set of primers. The amplified PCR product was digested by Hinf1; the bands were visualized under UV-light to observe the polymorphic locus by the size change of DNA fragments. The results revealed that the restriction analysis produced two fragments of 424 and 71 bp indicating the presence of kappa casein BB genotype (monomorphic) in all population. The present study is the first report on kappa casein genotype of Baggara cattle in South Darfur State, Sudan, which elucidated uniform and homozygous population for kappa casein B allele.

Genetic variation and population structure of the oriental fruit moth Grapholita molesta in Shanxi, a major pome fruits growing region in North China

Grapholita molesta, commonly known as the oriental fruit moth, is one of the most destructive fruit pests both in China and in other regions of the world. We examined the genetic diversity and population structures of G. molesta populations from 11 locations in a major pome fruit production region (Shanxi province) in North China using seven microsatellite markers and sequence variations in two mitochondrial genes. We found that G. molesta in the studied region exhibited high levels of genetic diversity. Among 271 individual insects examined using microsatellite markers, mean number of alleles ranged from 5.86 to 9.00 with average 8.01. Population structure analysis revealed that populations from the eleven sampling sites formed two clusters without apparent distance isolation. Cluster 1 consisted of eight populations distributed in five regions of the sampling sites, whereas Cluster 2 consisted of three populations distributed in two distant locations of the sampling sites. Genetic exchange analysis revealed that about half of the haplotypes were shared among over 90% individual insects from different regions. Our results indicated that the population structure and genetic exchange of G. molesta in the studied region might have been affected by limited dispersal ability of the insect, environmental condition, colonization history and human-mediated dispersal. These findings should provide useful information for the implementation of area-wide pest management and for further characterization of genetic variation and population structure of this economically important pest.

Characterization of Colletotrichum gloeosporioides, as the main causal agent of citrus anthracnose, and C. karstii as species preferentially associated with lemon twig dieback in Portugal

In the last two decades significant losses in citrus production in Portugal related to anthracnose symptoms have been recorded. These symptoms were attributed to Colletotrichum gloeosporioides, but preliminary population diversity evidence suggested that other Colletotrichum species could be involved in the disease. In this work, a field survey of the main citrus growing areas in Portugal was conducted and the pathogenicity of a group of Colletotrichum spp. isolates was studied along with morphological and genetic variability characterization [including Inter-Simple Sequence Repeats (ISSR) profiles and DNA sequence data of rDNA-ITS and β-tubulin 2 gene regions]. Colletotrichum karstii (from the C. boninense species complex) and C. gloeosporioides were identified from symptoms on leaves, branches, flowers and fruits of several citrus cultivars. However, C. acutatum, the species most commonly associated with citrus anthracnose in the Americas, was never detected. While C. gloeosporioides was isolated at higher frequency overall (87 %), C. karstii was more frequent in branches and leaves of lemon in specific geographic locations. Only C. gloeosporioides was detected in flowers. Colletotrichum karstii and C. gloeosporioides were pathogenic to sweet orange flowers and fruits and to leaves of sweet orange, mandarin and lemon, while reference C. acutatum citrus isolates were pathogenic to Key lime flowers and leaves.

Characterization of Genetic Variability and Population Structure of the Tick Amblyomma aureolatum (Acari: Ixodidae).

The hard tick Amblyomma aureolatum (Pallas) is a vector of the bacterium Rickettsia rickettsii, the etiologic agent of Brazilian spotted fever (BSF) in parts of Brazil. Despite its wide distribution in southeastern South America and its public health importance, there is no information about genetic variation of this species that might help to understand the epidemiology of BSF. Using data from eight microsatellite markers and ticks from six localities, we used a population genetics approach to test the hypothesis that tick populations from areas with the presence of R. rickettsii are genetically different from ticks from areas without R. rickettsii Contrary to expectations, we found low genetic structure between studied regions. Thus, the presence of R. rickettsii in the specific area is more likely correlated with ecological and the environmental conditions or due to unknown gene coding regions of A. aureolatum genome that would be related to R. rickettsii infection resistance.

Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses.

Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne alphavirus that has caused large outbreaks of severe illness in both horses and humans. New approaches are needed to rapidly infer the origin of a newly discovered VEEV strain, estimate its equine amplification and resultant epidemic potential, and predict human virulence phenotype. We performed whole genome single nucleotide polymorphism (SNP) analysis of all available VEE antigenic complex genomes, verified that a SNP-based phylogeny accurately captured the features of a phylogenetic tree based on multiple sequence alignment, and developed a high resolution genome-wide SNP microarray. We used the microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array- and sequence-based SNP calls, genotyped unsequenced isolates, and placed them on a phylogeny with sequenced genomes. The microarray successfully genotyped VEEV directly from tissue samples of an infected mouse, bypassing the need for viral isolation, culture and genomic sequencing. Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype.