Blast and download server for 959 Nematode Genomes

Scroll down for data download links for the assemblies in the drop-down list above.

PLEASE NOTE:

These are preliminary assemblies and should not be treated as draft/finished genomes. The assemblies may change often and data should only be used with the consent of the contact person listed.

Name: Ascaris suum from Jex 2011
Contact: Robin Gasser, Aaron Jex
Sequencing Centre: BGI
Assembly Version: 
Assembly Date: downloaded 11 Nov 2011

Abstract from the Nature paper at http://dx.doi.org/10.1038/nature10553

Parasitic diseases have a devastating, long-term impact on human health, 
welfare and food production worldwide. More than two billion people are 
infected with geohelminths, including the roundworms Ascaris (common 
roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), 
mainly in developing or impoverished nations of Asia, Africa and Latin 
America. In humans, the diseases caused by these parasites result in about 
135,000 deaths annually, with a global burden comparable with that of 
malaria or tuberculosis in disability-adjusted life years. Ascaris alone 
infects around 1.2 billion people and, in children, causes nutritional 
deficiency, impaired physical and cognitive development and, in severe 
cases, death. Ascaris also causes major production losses in pigs owing to 
reduced growth, failure to thrive and mortality. The Ascaris-swine model 
makes it possible to study the parasite, its relationship with the host, 
and ascariasis at the molecular level. To enable such molecular studies, we 
report the 273 megabase draft genome of Ascaris suum and compare it with 
other nematode genomes. This genome has low repeat content (4.4%) and 
encodes about 18,500 protein-coding genes. Notably, the A. suum secretome 
(about 750 molecules) is rich in peptidases linked to the penetration and 
degradation of host tissues, and an assemblage of molecules likely to 
modulate or evade host immune responses. This genome provides a 
comprehensive resource to the scientific community and underpins the 
development of new and urgently needed interventions (drugs, vaccines and 
diagnostic tests) against ascariasis and other nematodiases.

WormBase FTP site

Name: Bursaphelenchus xylophilus from Kikuchi 2011
Contact: Taisei Kikuchi, James Cotton
Sequencing Centre: Wellcome Trust Sanger Institute
Assembly Version: 
Assembly Date: downloaded 11 Nov 2011

From the abstract from the PLOS Pathogens paper at 

Bursaphelenchus xylophilus is the nematode responsible for a devastating 
epidemic of pine wilt disease in Asia and Europe, and represents a 
recent, independent origin of plant parasitism in nematodes, ecologically 
and taxonomically distinct from other nematodes for which genomic data is 
available. As well as being an important pathogen, the B. xylophilus 
genome thus provides a unique opportunity to study the evolution and 
mechanism of plant parasitism. Here, we present a high-quality draft 
genome sequence from an inbred line of B. xylophilus, and use this to 
investigate the biological basis of its complex ecology which combines 
fungal feeding, plant parasitic and insect-associated stages.

Bursaphelenchus data downloads

Name: Caenorhabditis species 11 (strain JU1373) from WashU
Contact: sclifton@watson.wustl.edu
Sequencing Centre: Genome Sequencing Center, Washington University
Assembly Version: nematodegenomes_v1 (release version)
Assembly Date: 2010-07-01

Comments: These data were produced by GSC as part of the ModENCODE 
project funded by NIH NHGRI) and are made available here by kind 
permission. Please contact Sandra W. Clifton 
 for general enquiries about the 
assembly. The GSC does intend to generate additional data for this 
species, and thus the assembly may change. Assembled using 454 
Sequencing and Newbler.

FTP link on wormbase

Name: Caenorhabditis species 5 (strain JU800) WormBase WS230 from genePool
Contact: sujai.kumar@ed.ac.uk, mark.blaxter@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: WS230
Assembly Date: 2011-09-12

Comments: The genome sequence of JU800 (Caenorhabditis species 5) is being
generated by the Blaxter lab in collaboration with Asher Cutter (Toronto).

Assembly version WS230 was made using one lane of hiseq2000 data - 300bp and 600 bp PE
abyss, velvet and clcbio were tried after removing bacterial contaminants
and clcbio had the best biological (i.e. alignments to known sequences) and
contig stats.

Caenorhabditis sp.5 genome data page

Name: Caenorhabditis species 5 CDS transcripts - MAKER2
Contact: sujai.kumar@ed.ac.uk, mark.blaxter@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: WS230
Annotation Version: MAKER2
Annotation Date: 2012-01-12

Comments: The genome sequence of JU800 (Caenorhabditis species 5) is being
generated by the Blaxter lab in collaboration with Asher Cutter (Toronto).

One annotation freeze was done by WormBase (and is available in release WS230
at c_sp5.WS230.cds_transcripts.fa.gz)
The WS230 annotation was done with Augustus without any EST or protein alignments.

This annotation freeze (MAKER2) was done using a two-pass MAKER2 pipeline
with a C. sp. 5 RNA-Seq assembly as an EST set, and C. briggsae + Swissprot
as a protein set. This transcript set has 40,813 predictions which
includes many hypothetical predictions without any evidence.

Caenorhabditis sp.5 genome data page

Name: PLEASE SEE NOTES-Caenorhabditis species 7 (strain JU1286) from WashU
Contact: sclifton@watson.wustl.edu
Sequencing Centre: Genome Sequencing Center, Washington University
Assembly Version: nematodegenomes_v1 (release version)
Assembly Date: 2010-07-01

Comments: These data were produced by GSC as part of the ModENCODE 
project funded by NIH NHGRI) and are made available here by kind 
permission. Please contact Sandra W. Clifton 
 for general enquiries about the 
assembly. The GSC does intend to generate additional data for this 
species, and thus the assembly may change. Assembled using 454 
Sequencing and Newbler

NOTE: Update as of 2011-07-16

There appears to be some cross-contamination of Caenorhabditis 
spp. 7/9 genomes.
Please proceed with caution.

FTP link on wormbase

Name: PLEASE SEE NOTES-Caenorhabditis species 9 (strain JU1422) from WashU
Contact: sclifton@watson.wustl.edu
Sequencing Centre: Genome Sequencing Center, Washington University
Assembly Version: nematodegenomes_v1 (release version)
Assembly Date: 2010-07-01

Comments: These data were produced by GSC as part of the ModENCODE 
project funded by NIH NHGRI) and are made available here by kind 
permission. Please contact Sandra W. Clifton 
 for general enquiries about the 
assembly. The GSC does intend to generate additional data for this 
species, and thus the assembly may change. Assembled using 454 
Sequencing and Newbler

NOTE: Update as of 2011-07-16

There appears to be some cross-contamination of Caenorhabditis
spp. 7/9 genomes.
Please proceed with caution.

FTP link on wormbase

Name: Dirofilaria immitis RNASeq assembly from GenePool and University of Basel v1_20110321
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.0
Assembly Date: 2011-03-21

Comments: Dirofilaria immitis is a filarial parasite of dogs.
This rnaseq assembly was made from male and female adult worms.

Illumina Solexa GAIIx paired end sequencing. The insert size was smaller than requested
(only 120bp)

TransABySS was used with kmers 23-47 in steps of 2 (23, 25, 27...)

Draft transcriptome assembly

Name: Dirofilaria immitis from GenePool and University of Basel v1.3
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh, and Fasteris
Assembly Version: 1.3
Assembly Date: 2011-09-01

Comments: Dirofilaria immitis is a filarial parasite of dogs.
This assembly was made from raw reads from which the
Wolbachia and mitochondrial sequences have been removed. 

Illumina Solexa GAIIx and HiSeq data. 180 bp, 340 bp paired end
and mate pairs (which were treated as single end reads)

CLC, Velvet and ABySS were all tried. The ABySS assembly had
the best contig stats and alignments to known filarial 
nematode proteins.

This assembly supersedes previous versions as some Wolbachia
contigs have been removed.

Draft genome assembly

Name: Dirofilaria immitis from GenePool and University of Basel v1.3 Maker 0.9 Transcripts
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh, and Fasteris
Assembly Version: 1.3
Assembly Release Date: 2011-09-01

Comments: Dirofilaria immitis is a filarial parasite of dogs.
This assembly was made from raw reads from which the
Wolbachia and mitochondrial sequences have been removed. 

The Maker pipeline was used to predict genes. This is the Maker
Transcripts fasta file produced by our Maker run 0.9

Draft Maker transcript predictions
Draft Maker protein predictions
Draft Maker GFF annotation

Name: Heligmosomoides polygyrus (Rick Maizels lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk, mark.blaxter@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.0
Assembly Date: 2010-08-23

Comments: GenePool will be generating additional data for this species
in the near future. Assembled from one lane of 50 bp paired end and
one lane of 100 bp paired end reads on a GAIIx using clc.

Name: Howardula aeoronymphium (Jaenicke lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk, mark.blaxter@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.0
Assembly Date: 2010-07-01

Comments: Howardula aoronymphium is a parasite of Drosophila.
The Blaxter lab is surveying the genome of this species in
collaboration with John jaenicke. This genome sequence assembly
is generated from initial data derived from nematodes isolated
from within Drosophila hosts. There is therefore significant
Drosophila genomic sequence in these contigs, so please do check
the phylum-of-origin of any interesting matches. GenePool will
be generating additional data for this species in the near future.
Assembled from one lane of GAIIx using clc

Draft genome assembly

Name: Litomosoides sigmodontis nuclear genome (Bain lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.1
Assembly Date: 2010-07-01

Comments: Litomosoides sigmodontis is a filarial parasite of 
rodents. The Blaxter lab is sequencing the genome of this species 
in collaboration with Simon Babayan and Judi Allen. This assembly 
was made from raw reads from which the Wolbachia and mitochondrial 
sequences had been removed. GenePool will be generating additional 
data for this species in the near future.

Assembled using 4 lanes of 50bp pe GAII data (100M reads)
First removed mitochondrial reads, then removed wolbachia contigs, 
and finally assembled using clc, velvet and abyss (the abyss 
assembly had the best contig stats and is released here)

Maker predictions done using brugia WS220 peptides, L sigmodontis cDNA assembly
and Brugia Augustus HMM models

Draft genome assembly
Draft maker gff predictions
Draft maker proteins fasta
Draft maker transcripts fasta

Name: Litomosoides sigmodontis mitochondrial genome (Bain lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.1
Assembly Date: 2010-07-01

Comments: Litomosoides sigmodontis is a filarial parasite of 
rodents. The Blaxter lab is sequencing the genome of this species 
in collaboration with Simon Babayan and Judi Allen. This assembly 
is just the mitochondrial genome.

Assembled using 4 lanes of 50bp pe GAII data (100M reads)
Assembled using velvet with very high kmer (45). Contigs
with high coverage were deemed putative wolbachia contigs.
3 such contigs hit Brugia mitochondrion, and their ends
were stitched together using pairing information.

Draft mitochondrion genome assembly

Name: Litomosoides sigmodontis transcriptome (Bain lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.1
Assembly Date: 2010-10

Comments: Litomosoides sigmodontis is a filarial parasite of 
rodents. The Blaxter lab is sequencing the genome of this species 
in collaboration with Simon Babayan and Judi Allen. 

This assembly was made from 454 transcriptome sequencing of
3 stages - adult male, adult female, and microfilaria, as described in
http://www.biomedcentral.com/1471-2164/11/571

Newbler 2.5 (with the -cdna -urt options) and MIRA 3.0 were used to generate
initial assemblies and CAP3 was used to combine contigs into a secondary
assembly and only those contigs were chosen that had evidence from both
Newbler and MIRA

Name: Litomosoides sigmodontis Wolbachia genome (Bain lab strain) from GenePool
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 1.1
Assembly Date: 2010-07-01

Comments: Litomosoides sigmodontis is a filarial parasite of 
rodents that harbours a Wolbachia endosymbiont. The Blaxter lab is 
sequencing the genome of this species in collaboration with Simon 
Babayan and Judi Allen. This assembly was made from raw reads 
selected on the basis that they match Wolbachia from other taxa. 
GenePool will be generating additional data for this genome in the 
near future.

Assembled using 4 lanes of 50bp pe GAII data (100M reads).
First removed mitochondrial reads, then assembled the rest
using velvet. The contigs that hit all known wolbachia
(with lenient settings) were used to reassemble the wolbachia
genome using velvet, abyss, and clc (the velvet assembly had
the best contig stats and is released here)

Draft wolbachia genome assembly

Name: Loa loa from Broad Institute / Nutman lab NIAID
Contact: Thomas Nutman TNUTMAN@niaid.nih.gov
Sequencing Centre: The Broad Institute of MIT and Harvard
Assembly Version: ADBU00000000.1  GI:285859101
Assembly Date: downloaded 27 Oct 2010

Comments: Loa loa. This filarial worm causes severe eye disorders in West 
and central Africa. The worm larvae are transmitted to humans through the 
Deer Fly or Mango Fly. Humans are the only known vector. The adult worms 
migrate throughout the subcutaneous tissue, occasionally crossing into 
subconjunctival tissues where it can be easily observed. Loa loa does not 
normally affect one’s vision but can be painful when moving about the 
eyeball or across the bridge of the nose. Treatment options include 
chemotherapy or surgical removal of the adult worms from the eye. 
These data were produced by The Broad Institute of MIT and Harvard in 
collaboration with Dr Tom Nutman of NIH.
The assembly is from a ~20 fold coverage using 454 reads. 
See http://www.ncbi.nlm.nih.gov/nuccore/ADBU00000000 for details.

Name: Meloidogyne floridensis (strain from David Lunt) from GenePool
Contact: sujai.kumar@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: nMf.1.0
Assembly Date: 2011-09-30

Comments:

Assembled using Illumina HiSeq 100bp pe sequencing (250 bp insert)
using Velvet, after several cleaning steps to remove bacterial
contaminants and co-bionts.

Name: Onchocerca ochengi from GenePool v0.3_20110126
Contact: gaganjot.kaur@ed.ac.uk
Sequencing Centre: GenePool, Edinburgh
Assembly Version: 0.3
Assembly Date: 2011-01-26

Comments: Onchocerca ochengi is a filarial parasite of cows.
This assembly was made from raw reads from which the
Wolbachia and mitochondrial sequences had been removed. 

Assembled using 4 lanes of 100bp pe GAIIx data (100M reads)
First removed reads mapping the Bos taurus genome. Then removed
mitochondrial reads, and wolbachia reads. Assembled using clc,
velvet and abyss (the clc assembly had the best contig stats
and most aligned sequences to known filarial nematode sequences
and is released here). The next assembly version is expected
to incorporate more checks (contamination and coverage checks)

Draft genome assembly

Name: Oscheis tipulae (derivatives of strain CEW1) from GenePool
Contact: sujai.kumar@ed.ac.uk, mark.blaxter@ed.ac.uk
Sequencing Centre: genePool, Edinburgh
Assembly Version: 1.1
Assembly Date: 2010-07-01

Comments: Oscheius tipulae is a free-living rhabditid. The Blaxter 
lab is sequencing this genome in collaboration with Marie Anne 
Felix of Paris. The current assembly is based on data deriving from 
CEW1, generated by GenePool, and Ju70, a CEW1 derivative strain, 
generated by the Felix lab.

Assembly Stats:

Max contig length
109671

Num contigs >200	Total bases in contigs >200
15455 			61786023

N50 for contigs >200	Contigs >200 in N50	GC contigs >200
13984			1209			0.449

Num contigs >1000	Total bases in contigs >1000
7218			58051798

N50 for contigs >1000	Contigs >1000 in N50	GC contigs >1000
15147			1081			0.447

Draft genome assembly

Name: Wuchereria bancrofti from Broad Institute / Nutman lab NIAID
Contact: Thomas Nutman TNUTMAN@niaid.nih.gov
Sequencing Centre: The Broad Institute of MIT and Harvard
Assembly Version: ADBV00000000.1  GI:285844741
Assembly Date: downloaded 27 Oct 2010

Comments: Wuchereria bancrofti. This parasitic filarial nematode is a causal 
agent of lymphatic filariasis, an infection of the lympatic system. This 
mosquito-borne disease affects over 120 million people, primarily in Africa. 
If the infection is left untreated it can develop into a debilitating 
condition called elephantiasis, marked by profound enlargement of the 
extremities.
The nematode life cycle involves two hosts. First stage larve, or 
microfilarae, live in the circulatory system. If transferred to a mosquito 
vector, the larvae transform into second stage larvae, or juveniles. 
Following a second transfer into a new human host, the larvae move through 
the lymphatic system into a regional node, normally in the legs or genital 
area. The larvae develop into adult worms over the course of a year, and each 
livebearing female can produce thousands of microfilarae.
These data were produced by The Broad Institute of MIT and Harvard in 
collaboration with Dr Tom Nutman of NIH.
The assembly is from a 'light skim' using 454 reads. 
See http://www.ncbi.nlm.nih.gov/nuccore/285844741 for details.