Data Mining of the Coffee Rust Genome

The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the genomic data

Molecular networks of pathogenicity control in Xanthomonas phaseoli pv. manihotis

Cassava (Manihot esculenta Crantz) is one the most important crops around the world due to its environmental resistance and industrial utility. Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of the cassava bacterial blight, the main bacterial disease of cassava. In Xanthomonas, several studies have been performed in the fields of transcriptomics, metabolomics, population genetics, and phylogenetics. However, few studies of gene expression profiles for pathogens in planta have been performed in the Xanthomonas genus, or in other plant pathogens. Moreover, few studies have analyzed the pathogenic system as whole. Systems biology is a new interdisciplinary field that has allowed to investigate organisms as a whole, where the totality of the system is greater than the independent addition of the parts. The scope of this thesis is to study the molecular mechanisms involved in pathogenicity of Xpm both in vitro and in planta. The gene expression profiles of mutants of Xpm related with molecular mechanisms of pathogenicity were studied in vitro. Furthermore, the interaction between cassava and Xpm in planta was also studied using gene expression profiles. The thesis is divided in three chapters. The first chapter responds to the need of having an updated review of network biology in bacterial pathogens and how this field of systems biology can help to understand the molecular mechanism of plant-pathogen interactions. The second chapter presents the first metabolic model of Xpm, reconstructed at a genome-scale, revealing important features of Xpm related with pathogenicity, virulence and bacterial defense. The final chapter analyzes the gene expression profiles of Xpm in planta during the interaction with cassavaLa yuca (Manihot esculenta Crantz) es uno de los cultivos más importantes alrededor del mundo debido a su resistencia ambiental y su utilidad industrial. Xanthomonas phaseoli pv. manihotis (Xpm) es el agente causal del añublo bacteriano de la yuca, la principal enfermedad de esta planta. En Xanthomonas, varios estudios han sido desarrollados en el campo de las ómicas, la genética de poblaciones y la filogenética. Sin embargo, pocos estudios de los perfiles de expresión de patógenos in planta han sido desarrollados en el género de Xanthomonas o en otros patógenos. Más aún, pocos estudios han analizado el sistema patogénico como un todo. La biología de sistemas es un nuevo campo interdisciplinario que ha permitido la investigación de los organismos como un todo, donde la totalidad del sistema es mayor que la adición separada de sus partes. El alcance de esta tesis es el estudiar los mecanismos moleculares involucrados en la patogenicidad de Xpm tanto in vitro como in planta. Los perfiles de expresión de los mutantes de Xpm relacionados con los mecanismos moleculares de patogenicidad fueron estudiados in vitro. Además, la interacción entre la yuca y Xpm in planta fue también estudiada usando perfiles de expresión. La tesis está dividida en tres capítulos. El primero responde a la necesidad de tener una revisión actualizada de la biología de redes en patógenos bacterianos y de cómo este campo de la biología de sistemas puede ayudar a entender los mecanismos moleculares de interacción planta-patógeno. El segundo capítulo presenta el primer modelo metabólico de Xpm, reconstruido a una escala genómica, revelando características importantes de Xpm relacionadas con la patogenicidad, la virulencia y la defensa bacteriana. El capítulo final analiza los perfiles de expresión génica de Xpm in planta durante la interacción con la yucaDoctor en Ciencias - BiologíaDoctorad

Molecular networks of pathogenicity control in Xanthomonas phaseoli pv. manihotis

Cassava (Manihot esculenta Crantz) is one the most important crops around the world due to its environmental resistance and industrial utility. Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of the cassava bacterial blight, the main bacterial disease of cassava. In Xanthomonas, several studies have been performed in the fields of transcriptomics, metabolomics, population genetics, and phylogenetics. However, few studies of gene expression profiles for pathogens in planta have been performed in the Xanthomonas genus, or in other plant pathogens. Moreover, few studies have analyzed the pathogenic system as whole. Systems biology is a new interdisciplinary field that has allowed to investigate organisms as a whole, where the totality of the system is greater than the independent addition of the parts. The scope of this thesis is to study the molecular mechanisms involved in pathogenicity of Xpm both in vitro and in planta. The gene expression profiles of mutants of Xpm related with molecular mechanisms of pathogenicity were studied in vitro. Furthermore, the interaction between cassava and Xpm in planta was also studied using gene expression profiles. The thesis is divided in three chapters. The first chapter responds to the need of having an updated review of network biology in bacterial pathogens and how this field of systems biology can help to understand the molecular mechanism of plant-pathogen interactions. The second chapter presents the first metabolic model of Xpm, reconstructed at a genome-scale, revealing important features of Xpm related with pathogenicity, virulence and bacterial defense. The final chapter analyzes the gene expression profiles of Xpm in planta during the interaction with cassavaLa yuca (Manihot esculenta Crantz) es uno de los cultivos más importantes alrededor del mundo debido a su resistencia ambiental y su utilidad industrial. Xanthomonas phaseoli pv. manihotis (Xpm) es el agente causal del añublo bacteriano de la yuca, la principal enfermedad de esta planta. En Xanthomonas, varios estudios han sido desarrollados en el campo de las ómicas, la genética de poblaciones y la filogenética. Sin embargo, pocos estudios de los perfiles de expresión de patógenos in planta han sido desarrollados en el género de Xanthomonas o en otros patógenos. Más aún, pocos estudios han analizado el sistema patogénico como un todo. La biología de sistemas es un nuevo campo interdisciplinario que ha permitido la investigación de los organismos como un todo, donde la totalidad del sistema es mayor que la adición separada de sus partes. El alcance de esta tesis es el estudiar los mecanismos moleculares involucrados en la patogenicidad de Xpm tanto in vitro como in planta. Los perfiles de expresión de los mutantes de Xpm relacionados con los mecanismos moleculares de patogenicidad fueron estudiados in vitro. Además, la interacción entre la yuca y Xpm in planta fue también estudiada usando perfiles de expresión. La tesis está dividida en tres capítulos. El primero responde a la necesidad de tener una revisión actualizada de la biología de redes en patógenos bacterianos y de cómo este campo de la biología de sistemas puede ayudar a entender los mecanismos moleculares de interacción planta-patógeno. El segundo capítulo presenta el primer modelo metabólico de Xpm, reconstruido a una escala genómica, revelando características importantes de Xpm relacionadas con la patogenicidad, la virulencia y la defensa bacteriana. El capítulo final analiza los perfiles de expresión génica de Xpm in planta durante la interacción con la yucaDoctor en Ciencias - BiologíaDoctorad

Annotation of a hybrid partial genome of the Coffee Rust (Hemileia vastatrix) contributes to the gene repertoire catalogue of the Pucciniales

Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333Mb was built based on the 8 isolates; this assembly was used for subsequent analyses.Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3,921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates

The Type VI Secretion System of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

Abstract Background: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout mutagenesis, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.</jats:p

The Type VI Secretion System of&amp;nbsp;Xanthomonas&amp;nbsp;phaseoli pv. manihotis&amp;nbsp;is involved in virulence and&amp;nbsp;in&amp;nbsp;vitro&amp;nbsp;motility

Abstract Background: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.</jats:p

The Type VI Secretion System of Xanthomonas Phaseoli pv. Manihotis is Involved in Virulence and in vitro Motility

Abstract Background: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout mutagenesis, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.</jats:p