Exploring the Genome of <i>Trypanosoma vivax</i> through GSS and <i>In Silico</i> Comparative Analysis

Guerreiro, Luana Tatiana Albuquerque; Souza, Sindoval Silva de; Wagner, Glauber; Souza, Edson A De; Mendes, Pablo N.; Campos, Linair Maria; Barros, Lígia; Pires, Paulo F.; Campos, María Luiza Machado; Grisard, Edmundo C.; Dávila, Alberto M. R.

doi:10.1089/omi.2005.9.116

Cited by 4 publications

(3 citation statements)

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“…OrthoMCL comparisons [69] were performed between Phytomonas EM1 and HART1, and four other trypanosomatids: L. major [29], T. brucei [28], T. cruzi [30] and Trypanosoma vivax [70] (Materials and Methods). This predicted 22,706 clusters of orthologous genes.…”

Section: Resultsmentioning

confidence: 99%

“…We identified orthologous genes between Phytomonas EM1 and HART1, and 4 other trypanosomatids: L. major [29], T. brucei [28], T. cruzi [30] and T. vivax [70] (Tritryp release 2.1). Each pair of annotated genes was aligned with the Smith-Waterman algorithm, and alignments with a score higher than 300 (BLOSUM62, gapo = 10, gape = 1) were retained.…”

Section: Methodsmentioning

confidence: 99%

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The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

et al. 2014

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Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

et al. 2014

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“…Nowadays, STINGRAY is hosting more than 20 different projects, among them the T. vivax (GSS and EST) [35], Bothrops jararaca (EST) [36], Lutzomyia longipalpis (EST) [37,38], Taenia solium (EST) [39] and Trypanosoma rangeli (GSS, EST and ORESTES) [40]. The main advantage of STINGRAY over related systems is its larger and flexible workflow on which advanced users or annotators are able to fine-tune the parameters of some programs to extract the maximum of valuable information and knowledge from their sequences.…”

Section: Discussionmentioning

confidence: 99%

STINGRAY: system for integrated genomic resources and analysis

et al. 2014

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BackgroundThe STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms.FindingsSTINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation.ConclusionSTINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

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Genome Survey Sequence Analysis and Identification of Homologs of Major Surface Protease (gp63) Genes inTrypanosoma rangeli

Ferreira

Ruiz

Dias

et al. 2010

Vector-Borne and Zoonotic Diseases

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In this study, 222 genome survey sequences were generated for Trypanosoma rangeli strain P07 isolated from an opossum (Didelphis albiventris) in Minas Gerais State, Brazil. T. rangeli sequences were compared by BLASTX (Basic Local Alignment Search Tool X) analysis with the assembled contigs of Leishmania braziliensis, Leishmania infantum, Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Results revealed that 82% (182/222) of the sequences were associated with predicted proteins described, whereas 18% (40/222) of the sequences did not show significant identity with sequences deposited in databases, suggesting that they may represent T. rangeli-specific sequences. Among the 182 predicted sequences, 179 (80.6%) had the highest similarity with T. cruzi, 2 (0.9%) with T. brucei, and 1 (0.5%) with L. braziliensis. Computer analysis permitted the identification of members of various gene families described for trypanosomatids in the genome of T. rangeli, such as trans-sialidases, mucin-associated surface proteins, and major surface proteases (MSP or gp63). This is the first report identifying sequences of the MSP family in T. rangeli. Multiple sequence alignments showed that the predicted MSP of T. rangeli presented the typical characteristics of metalloproteases, such as the presence of the HEXXH motif, which corresponds to a region previously associated with the catalytic site of the enzyme, and various cysteine and proline residues, which are conserved among MSPs of different trypanosomatid species. Reverse transcriptase-polymerase chain reaction analysis revealed the presence of MSP transcripts in epimastigote forms of T. rangeli.

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Exploring the Genome of Trypanosoma vivax through GSS and In Silico Comparative Analysis

Cited by 4 publications

References 20 publications

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

The Streamlined Genome of Phytomonas spp. Relative to Human Pathogenic Kinetoplastids Reveals a Parasite Tailored for Plants

STINGRAY: system for integrated genomic resources and analysis

Genome Survey Sequence Analysis and Identification of Homologs of Major Surface Protease (gp63) Genes inTrypanosoma rangeli

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