Examinando por Autor "Moyano, Tomás C."

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    The Botrytis cinerea Gene Expression Browser
    (MDPI, 2023-01) Pérez-Lara, Gabriel; Moyano, Tomás C.; Vega, Andrea; Larrondo, Luis F.; Polanco, Rubén; Álvarez, José M.; Aguayo, Daniel; Canessa, Paulo
    For comprehensive gene expression analyses of the phytopathogenic fungus Botrytis cinerea, which infects a number of plant taxa and is a cause of substantial agricultural losses worldwide, we developed BEB, a web-based B. cinerea gene Expression Browser. This computationally inexpensive web-based application and its associated database contain manually curated RNA-Seq data for B. cinerea. BEB enables expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcript levels, without requiring advanced computational skills. BEB also provides details of each experiment and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, including, for instance, the determination of differentially expressed genes. The BEB implementation is based on open-source computational technologies that can be deployed for other organisms. In this case, the new implementation will be limited only by the number of transcriptomic experiments that are incorporated into the platform. To demonstrate the usability and value of BEB, we analyzed gene expression patterns across different conditions, with a focus on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, providing the first comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen. We expect this tool to be broadly useful in B. cinerea research, providing a basis for comparative transcriptomics and candidate gene identification for functional assays. © 2023 by the authors.
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    Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans
    (Nature Publishing Group, 2019-12) Vidal, Elena A.; Moyano, Tomás C.; Bustos, Bernabé I.; Pérez-Palma, Eduardo; Moraga, Carol; Riveras, Eleodoro; Montecinos, Alejandro; Azócar, Lorena; Soto, Daniela C.; Vidal, Mabel; Genova, Alex Di; Puschel, Klaus; Nürnberg, Peter; Buch, Stephan; Hampe, Jochen; Allende, Miguel L.; Cambiazo, Verónica; González, Mauricio; Hodar, , Christian; Montecino, Martín; Muñoz-Espinoza, Claudia; Orellana, Ariel; Reyes-Jara, Angélica; Travisany, Dante; Vizoso, Paula; Moraga, Mauricio; Eyheramendy, Susana; Maass, Alejandro; Ferrari, Giancarlo V. De; Miquel, Juan Francisco; Gutiérrez, Rodrigo A.
    Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 6 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations. © 2019, The Author(s).