Ontology highlight
ABSTRACT:
PROVIDER: PRJNA398351 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5934425_1.fastq.gz | Fastqsanger.gz | |||
| SRR5934425_2.fastq.gz | Fastqsanger.gz | |||
| SRR5934426_1.fastq.gz | Fastqsanger.gz | |||
| SRR5934426_2.fastq.gz | Fastqsanger.gz | |||
| SRR5934427_1.fastq.gz | Fastqsanger.gz |
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Project description:Trypanosoma vivax is a major pathogen of domestic cattle and wildlife across sub-Saharan Africa. For many years, the WTSI has had a research interest in developing a genome sequence for T. vivax, as part of a wider programme concerning African trypanosome parasites of Humans and animals. In 2012 a draft genome sequence for T. vivax Y486 was published by the WTSI and our collaborators in comparison with related species, T. brucei and T. congolense. This study identified numerous putative genes in T. vivax that have no known affinity and are therefore species-specific. A related transcriptomic study confirmed that some of these putative genes are transcribed, but lacked accuracy and was based on a single parasite life stage only. Until recently, it has not been possible to culture different T. vivax life stages in refined media. There is now the opportunity to use new approaches to produce whole cell RNA for both insect and bloodstream parasite stages. We sequence stage-specific cDNA and identify stage-specific genes, and compare these features with similar data already available for T. brucei and T. congolense, which display substantial differences in their developmental cycles. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-03-07 | E-ERAD-100 | biostudies-arrayexpress
Project description:Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole genome sequencing (30X coverage). This analysis revealed over 18,261 single nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Sal1 strain obtained in 1970. This full-genome sequence of a P. vivax isolate, the second overall and first of an uncultured patient isolate, shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous to synonymous SNPs encode two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in P. falciparum. This analysis provides a new data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies. Genome DNA from Peruvian P. vivax Isolate IQ07 vs. Reference Sal1
2010-10-02 | E-GEOD-23982 | biostudies-arrayexpress
Project description:The parasitic flagellate Trypanosoma vivax is a cause of animal trypanosomiasis across Africa and South America. The parasite has a digenetic life cycle, passing between mammalian hosts and insect vectors, and a series of developmental forms adapted to each life cycle stage. Transcriptomic and proteomic studies of the related parasites T. brucei and T. congolense have shown how gene expression is regulated during their development. New methods for in vitro culture of the T. vivax insect stages have allowed us to describe global gene expression throughout the complete T. vivax life cycle for the first time. We combined transcriptomic and proteomic analysis of each life stage using RNA-seq and mass spectrometry respectively, to identify genes with patterns of preferential transcription or expression. While T. vivax is similar to related species in several ways, (e.g. developmental regulation of energy metabolism, restricted expression of a dominant variant antigen, and expression of ‘Fam50’ proteins in the insect mouthparts), we identify significant differences in gene expression affecting metabolism in the fly and a suite of T. vivax-specific genes with predicted cell-surface expression that are preferentially expressed in the mammal (‘Fam29, 30’) or the vector (‘Fam34, 35, 43’). Thus, T. vivax differs significantly from other African trypanosomes in the developmentally-regulated proteins it expresses on its cell surface and thus, in the structure of the host-parasite interface. These unique features may yet explain the species differences in life cycle and could, in the shape of bloodstream-stage proteins that do not undergo antigenic variation, provide targets for therapy.
2015-07-20 | PXD001617 | Pride
Project description:Unlike in Asia and Latin America, Plasmodium vivax infections were rare in Sub-Saharan Africa due to the absence of the Duffy blood group antigen (Duffy Antigen), the only known erythrocyte receptor for the P. vivax merozoite invasion ligand, Duffy Binding Protein 1 (DBP1). However, P. vivax infections have been documented in Duffy-negative individuals throughout Africa, suggesting that P. vivax may use ligands other than DBP1 to invade Duffy-negative erythrocytes through other receptors. To identify potential P. vivax ligands, we compared parasite gene expression in Saimiri and Aotus monkey erythrocytes infected with P. vivax Salvador I (Sal I). DBP1 binds Aotus but does not bind to Saimiri erythrocytes, and thus P. vivax Sal I must invade Saimiri erythrocytes independently of DBP1. Comparing RNA sequencing (RNAseq) data for late stage infections in Saimiri and Aotus erythrocytes when invasion ligands are expressed, we identified genes that belong to tryptophan-rich antigen and MSP3 families that were more abundantly expressed in Saimiri infections as compared to Aotus infections. These genes may encode potential ligands responsible for P. vivax infections of Duffy-negative Africans.
2019-04-17 | GSE125284 | GEO
Project description:Trypanosoma vivax Transcriptome or Gene expression
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Project description:Trypanosoma vivax Y486 bloodstream stage RNAseq
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Project description:Trypanosoma vivax strain:Lins Genome sequencing and assembly
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Project description:Trypanosoma vivax strain:IL1392 Genome sequencing and assembly
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