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Papers by Claudia Vitorello

Research Square (Research Square), Nov 1, 2019

BackgroundThe white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil... more BackgroundThe white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute

Research Square (Research Square), Oct 25, 2019

Puccinia kuehniiis an obligate biotrophic fungus that infects sugarcane leaves causing a disease ... more Puccinia kuehniiis an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak in Australia. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by the stress induced byP. kuehnii. Here we investigated changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at 0, 12, 24, 48 hours after inoculation (hai), 5 and 12 days after inoculation (dai). Ade novotranscriptome was assembled with preprocessed reads, filtering out potential fungal sequences to focus on plant transcripts. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 hai and 12 dai, coinciding with the events of spore germination, haustoria post-penetration and post-sp...

Additional file 2. RGA Dataset.

Nature, Jan 13, 2000

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically i... more Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecul...

Nature, 2002

Whole-genome comparisons between Xac and Xcc We compared the genomes at the nucleotide level usin... more Whole-genome comparisons between Xac and Xcc We compared the genomes at the nucleotide level using the program MUMmer with default values. At the amino acid level the genomes were compared using programs developed by our bioinformatics team. Genes g and h were considered orthologues if h is the best BLASTP hit for g and vice versa, with e-values less than or equal to 10 220. A gene was considered strain-specific if it had no hits with an e-value 10 25 or less.

Brazilian Journal of Medical and Biological Research, 2004

We report novel features of the genome sequence of Leptospira interrogans serovar Copenhageni, a ... more We report novel features of the genome sequence of Leptospira interrogans serovar Copenhageni, a highly invasive spirochete. Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in mammals. Genomic sequence analysis reveals the presence of a competent transport system with 13 families of genes encoding for major transporters including a three-member component efflux system compatible with the long-term survival of this organism. The leptospiral genome contains a broad array of genes encoding regulatory system, signal transduction and methyl-accepting chemotaxis proteins, reflecting the organism's ability to respond to diverse environmental stimuli. The identification of a complete set of genes encoding the enzymes for the cobalamin biosynthetic pathway and the novel coding genes related to lipopolysaccharide biosynthesis should bring new light to the study of Leptospira physiology. Genes related to toxins, lipoproteins and several surface-exposed proteins may facilitate a better understanding of the Leptospira pathogenesis and may serve as potential candidates for vaccine.

Additional file 1. PRGdb Dataset.

Additional file 3: Figure S1. Distribution of RGA candidates predicted from COMPGG de novo unique... more Additional file 3: Figure S1. Distribution of RGA candidates predicted from COMPGG de novo unique transcript sequences along 10 chromosomes of Sorghum bicolor genome. Figure S2. Distribution of RGA candidates predicted from AP85–441 S. spontaneum along 10 chromosomes of Sorghum bicolor genome. Figure S3. Distribution of RGA candidates predicted from R570 sugarcane cultivar monoploid genome along 10 chromosomes of Sorghum bicolor genome. Figure S4. Distribution of RGA candidates predicted from Sorghum bicolor along 10 chromosomes of its genome. Figure S5. Shared synteny view of the four most frequent RGA subgroups along the chromosomes of three references of sugarcane. Figure S6. RGA ortholog relationships among four references of sugarcane. Figure S7. Experimental design used in this work. Table S1. General RNAseq data statistics used in this study. Table S2. Overview of the proportion of predicted RGAs and RGADEs in the chromosomes in relation to the total of correspondent predicti...

☯ These authors contributed equally to this work. ‡ These authors also contributed equally to thi... more ☯ These authors contributed equally to this work. ‡ These authors also contributed equally to this work.

Achieving sustainable cultivation of sugarcane Volume 2

PLOS ONE

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize ... more Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shapi...

Leifsonia xyli subsp. xyli (Lxx) causes ratoon stunting disease (RSD), a major worldwide disease ... more Leifsonia xyli subsp. xyli (Lxx) causes ratoon stunting disease (RSD), a major worldwide disease of sugarcane. Formerly classified as Clavibacter xyli subsp. xyli, Lxx is a fastidious member of the GC-rich Actinomycetales., a taxonomic order that comprises two other genera of plant pathogens of great agricultural impact. In this review we present some interesting features of the genome of Lxx with emphasis on pathogenicity. Most striking is the observation that Lxx has a relatively large number of pseudogenes suggestive of an ongoing process of genome decay. It has been proposed that Lxx was once a free-living bacterium that is now restricted to the xylem as a consequence or cause of the accumulation of pseudogenes. This point stems from the observation that although Lxx has only been detected inhabiting the xylem of sugar cane, it carries several genes typical of free-living organism. In this review we also discuss the relevance of lateral gene transfer in the acquisition of a few ...