Trypanosoma vivax is a major livestock pathogen in Africa and some South American countries. Despite the severe disease it causes, T. vivax remains largely unstudied. It is known that T. vivax differs from the Human and animal pathogen T. brucei in some important respects, including life cycle and host range. Therefore, a comparison of trypanosome genomes could help to explain the genetic causes of their fundamental biology.
The Wellcome Trust Sanger Institute's Pathogen Genomics group has carried out a partial genome shotgun of T. vivax strain Y486, producing a high-quality draft genome sequence with sequence coverage of 5x. The genome comprises 41,775,787bp, arranged into 11 pseudochromosomes, based on the T. brucei karyotype. However, as the precise karyotype of T. vivax Y486 is not known, we have also assembled the data de novo producing 280 scaffolds from 1828 sequence contigs. The genome sequence contains 11870 predicted genes.
Nine telomeres and their upstream regions were selected from a large-insert BAC library and sequenced using a whole shotgun approach. These sequences can be accessed through our ftp site.
Phylogenetic analyses of all gene families encoding proteins with predicted cell-surface roles in T. vivax have been carried out in comparison with T. congolense and T. brucei. This has identified 23 unique cell-surface gene families in T. vivax, as well as many significant changes to families shared in all three species. These data can be accessed through GeneDB.
GeneDB has been funded by Wellcome Trust to provide full curation support for kinetoplastida genomes to meet the needs of the community. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.
A manuscript has been prepared describing the genome of T. vivax Y486 and this will be published shortly. The genome sequence is available for use without restriction. However, the annotation is pro-actively updated and curated. If you find the this resource helpful in your research, acknowledging the project in your publications will help insure its longevity.
» Trypanosoma vivax on GeneDB
Rolling releases of T. vivax Y486 annotation
Download the latest annotation (gff3 files generated each month):
FTP - Rolling releases: current GFF3 'Tvivax' files.
Note: Genome sequence for T. vivax Y486 is still v2 (the same currently available at TriTrypDB). Genome sequence (fasta files) can also be downloaded from the ftp link above.
Comparative analysis of surface-expressed gene families