Analise in silico e in vivo da diversidade nucleotidica em Coffea ssp.

Polimorfismos de modificações nucleotídicas (SNPs ? Single Nucleotide Polymorphisms, INDELs ? Insertion / Deletions) têm uma alta freqüência nos genomas da maioria dos organismos, incluindo plantas. Eles vêm se tornando a escolha principal de marcador para trabalhos de melhoramento, genotipagem e diagnóstico. A identificação destes polimorfismos irá fornecer marcadores que poderão ser utilizados para o mapeamento genético, estudos de genética de população e de associação. Portanto, os objetivos deste trabalho foram: 1) identificar in silico SNPs e INDELS existentes em seqüências de ESTs disponíveis; e 2) analisar a diversidade nucleotídica em Coffea spp. Um pipeline para identificação de SNPs e INDELs foi desenvolvido utilizando seqüências de ESTs disponíveis de Coffea spp. Foi utilizado uma estratégia para detecção de SNPs em dentro de 23.019 contigs. Um total 23.062 SNPs e 2.165 INDELS foram encontrados em 5184 contigs que continham pelo menos quatro ESTs. Analises in silico permitiram a identificação de diferentes alelos de C. canephora e C. eugenioides que estão presentes em C. arabica. A maioria dos ESTs de C. arabica vieram de apenas dois alelos, uma evidência molecular sobre a especiação de C. arabica. De acordo com essas análises cerca de 55% das seqüências de C. arabica são derivadas do genoma de C. eugenioides e 45% de C. canephora. Além disso, foi possível observar que o genoma de C. eugenioides contribui principalmente para genes relacionados a metabolismo basal, enquanto que os genes de C. canephora estão envolvidos com sinais de tradução e regulação da expressão gênica. Análises in vivo estão sendo realizadas através do sequenciamento de diversos genes em 24 genótipos de Coffea sendo 12 de C. arabica, 9 de C. canephora e três de outras espécies de Coffea, para uma analise maior da diversidade nucleotídica do gênero. Resultados referentes ao sequenciamento do gene de sacarose fosfato sintase (SPS) apresentaram 21 polimorfismos, sendo a maioria interespecíficos (C. arabica, C. canephora, C. eugenioides e C. racemosa). Para os genótipos de C. canephora foram observados nove polimorfismos intraespecíficos. Já os polimorfismos encontrados entre os genótipos de C. arabica forma os mesmos detectados entre C. canephora e C. eugenioides

Resistência do tipo antibiose a ninfas de Tibraca limbativentris (Stal, 1860) (Heteroptera: Pentatomidae) em variedades de arroz.

O percevejo-do-colmo (Tibraca limbativentris Stal, 1860) é uma importante praga do arroz no Brasil. O uso de variedades resistentes a esse inseto é uma ferramenta importante para o seu controle. O experimento foi conduzido em casa de vegetação na Embrapa Arroz e Feijão. Foi avaliada resistência tipo antibiose em ninfas de T. limbativentris em 16 variedades de arroz em delineamento experimental de blocos casualizados em oito repetições. Os caracteres utilizados para detectar indícios de resistência do tipo antibiose foram: número de ninfas vivas, massa seca (mg)/ninfas, superfície corporal/mm2, índice de sobrevivência e desenvolvimento e dias de vida das ninfas. Realizaram-se três tipos de análises: a) considerando somente os dados obtidos nas repetições avaliadas aos 7, 13, 21 e 26 dias após a infestação; b) considerando somente os dados das quatro repetições avaliadas aos 35 dias após a infestação e c) considerando os dados obtidos conjuntamente nas oito repetições. Conclui-se que as variedades Arroz Comum e Desconhecido Branco, principalmente a primeira, evidenciam possuir características que lhes confere determinado grau de resistência do tipo antibiose a ninfas de T. limbativentris

The Genome Sequence Of Leishmania (leishmania) Amazonensis: Functional Annotation And Extended Analysis Of Gene Models

We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment. © The Author 2013.206567581(2010) Control of the Leishmaniasis WHOTechnical Report Series, , WHO. WHO Press: GenevaLainson, R., Shaw, J.J., (1987) The leishmaniases in biology and medicine. Evolution, classification and geographical distributionBates, P.A., Transmission of Leishmania metacyclic promastigotes by phlebotomine sand flies (2007) Int. J. 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The Genome Sequence of Leishmania (Leishmania) amazonensis: Functional Annotation and Extended Analysis of Gene Models

We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3'-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. the model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. the analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade Federal de São Paulo, EPM UNIFESP, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilLNBio CNPEM, Lab Nacl Biociencias, Campinas, SP, BrazilLGE UNICAMP, Lab Genom & Expressao, Campinas, SP, BrazilInst Agron Campinas, Ctr Pesquisa & Desenvolvimento Recursos Geneti Ve, Campinas, SP, BrazilUniv Calif San Diego, Sch Med, Dept Pediat, San Diego, CA 92103 USAUniversidade Federal de São Paulo, UNIFESP, Dept Ciencia & Tecnol, Sao Jose Dos Campos, BrazilUniv N Carolina, Sch Med, Dept Genet, Chapel Hill, NC USAUniv Fed Minas Gerais, ICB UFMG, Inst Ciencias Biol, Dept Biol Geral, Belo Horizonte, MG, BrazilUniversidade Federal de São Paulo, EPM UNIFESP, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, BR-04023062 São Paulo, BrazilUniversidade Federal de São Paulo, UNIFESP, Dept Ciencia & Tecnol, Sao Jose Dos Campos, BrazilFAPESP: 07/50551-2FAPESP: 10/19335-4Web of Scienc

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm

Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8

Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups (AGs). One of these, AG8, is a devastating pathogen causing bare patch of cereals, brassicas and legumes. R. solani is a multinucleate heterokaryon containing significant heterozygosity within a single cell. This complexity posed significant challenges for the assembly of its genome. We present a high quality genome assembly of R. solani AG8 and a manually curated set of 13,964 genes supported by RNA-seq. The AG8 genome assembly used novel methods to produce a haploid representation of its heterokaryotic state. The whole-genomes of AG8, the rice pathogen AG1-IA and the potato pathogen AG3 were observed to be syntenic and co-linear. Genes and functions putatively relevant to pathogenicity were highlighted by comparing AG8 to known pathogenicity genes, orthology databases spanning 197 phytopathogenic taxa and AG1-IA.We also observed SNP-level “hypermutation” of CpG dinucleotides to TpG between AG8 nuclei, with similarities to repeat-induced point mutation (RIP). Interestingly, gene-coding regions were widely affected along with repetitive DNA, which has not been previously observed for RIP in mononuclear fungi of the Pezizomycotina. The rate of heterozygous SNP mutations within this single isolate of AG8 was observed to be higher than SNP mutation rates observed across populations of most fungal species compared. Comparative analyses were combined to predict biological processes relevant to AG8 and 308 proteins with effector-like characteristics, forming a valuable resource for further study of this pathosystem. Predicted effector-like proteins had elevated levels of non-synonymous point mutations relative to synonymous mutations (dN/dS), suggesting that they may be under diversifying selection pressures. In addition, the distant relationship to sequenced necrotrophs of the Ascomycota suggests the R. solani genome sequence may prove to be a useful resource in future comparative analysis of plant pathogens

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph