Data Access
Release 1.0 [09 August 2012]
[please see below centre for data access policy]
BLAST server
Nucleotide blast server
Search the nuclear genome and assembled transcriptome data with BLAST.
Nuclear Genome Browser
Genome Browser
Genome nAv1.0; Annotation nAv1.0.1
Assembly and annotation data downloads
Nuclear Assembly Freeze nAv.1.0
A. viteae nuclear genome assembly nAv.1.0 [nucleotide fasta, gzip]
Nuclear Annotation Freeze nAv.1.0.1
nAv.1.0.1 gene models and annotations
[gff, gzip]
Nuclear Annotation Freeze nAv.1.0.1 proteins
nAv.1.0.1 protein predictions
[protein fasta, gzip]
Nuclear Annotation Freeze nAv.1.0.1 transcripts
nAv.1.0.1 transcript predictions
[nucleotide fasta, gzip]
Mitochondrial Assembly Freeze mAv.1.0
Raw Data Downloads
Illumina Genome data : [Available soon]
Naming Conventions
We call the nuclear genome nAv, and the mitochondrial genome mAv. We version the assembly using the notation X.Y, where X is the version of the primary contigs used and Y a secondary version number indicating additional scaffolding or other improvement work has been performed. Thus nAv.1.0 is the primary assembly version 1. We also version annotations, so a gene set prediction based on nAv.1.0 is called nAv.1.0.1, etc.
We are committed to improving these assemblies, so please do tell us if you find issues or errors, and do watch out for updates.
About Acanthocheilonema viteae
[image: A. viteae lifecycle; from http://www.uni-giessen.de]
Acanthocheilonema viteae is a filarial nematode parasite of rodents. It is widely used as a model for human filariases. Importantly, A. viteae lacks the Wolbachia bacterial endosymbiont found in most human-infective filarial nematodes. Thus this species has become central in efforts to understand the role of the Wolbachia in the nematode-bacterial symbiosis, and in particular its possible role in immune evasion. The Wolbachia is also a drug target in nematodes that carry this symbiont, so work on A. viteae can also help to disentangle anti-nematode and anti-symbiont effects.
The genome sequence of A. viteae will assist in these efforts by offering a reference platform against which responses to drugs and the immune stystem can be measured, and a complete catalogue of the genes (and thus proteins) of the parasite. This catalogue can be screened and investigated using computer tools, enhancing the specificity of directed research, and ensuring that the whole of the parasites' capacities are considered.
Data release and publication
The data are freely downloadable here and through the public sequence repositories. We intend to publish a general overview of the genome of A. viteae, its transcriptome, and its relationship to other nematodes using these data. If you would like to collaborate on that project please do contact [email protected].
We ask that you do not use these data for global summary publications in advance of our genome manuscript publication, but are happy to assist you in directed investigations of genes and gene families of interest.
Genome Team
The A. viteae genome was sequenced from material supplied by Kenneth Pfarr. Sequencing was performed by the GenePool Genomics Facility, University of Edinburgh. Assembly and annotation of the genome was performed by Georgios Koutsovoulos (assisted by Sujai Kumar and Alex Marshall).
Collaborators
Kenneth Pfarr (1)
Mark Blaxter (2,3)
Georgios Koutsovoulos (2)
Sujai Kumar (2)
Alex Marshall (2,3)
(1) Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn Medical Center, Sigmund-Freud-Str. 25, Building 320, D-53105 Bonn, Germany.
(2) Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
(3) The GenePool Genomics Facility, School of Biological Sciences, University of Edinburgh, EH9 3JT, UK
Funding
This work is part of the EU-funded programme "Enhancing Protective Immunity Against Filariasis".
Links
The Blaxter Laboratory
NEMBASE4
959 Nematode Genomes Initiative
BaNG Nematode Genomes
Filaria-EU
The GenePool Genomics Facility
Pfarr Laboratory