1000 Nematode Genomes Initiative

Model Organism: Worms Scientific Discussion
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Dear Nematode Genomes Community

959 Nematode Genomes http://www.nematodes.org/nematodegenomes/

There are ~23,000 described species of nematodes, and an estimated 2-10 million species exist. Genomics research on nematodes (particularly Caenorhabditis elegans) has delivered important information on core biological processes and underpinned advances in biomedical science. Adding additional nematode genomes to that of C. elegans will allow the specific instance of C. elegans to be contextualised, and will we hope feed research on comparative genomics of nematodes, the evolutionary biology of genome change, and the biology of the (many) parasitic nematodes, amongst other fields. Many centres are engaged in genome and transcriptome sequencing of target nematodes (we have counted over 60 species with significant sequencing efforts underway). This unprecedented surge in nematode genomics offers an opportunity for coordinated and targeted analyses: either bringing experts on one particular process, pathway or gene family together to examine diversity across species, or nucleating interest groups focussing on particular clades of the nematode tree.

We are initiating a drive for a large number* of additional nematode genomes to be sequenced, and inviting everyone interested to make their plans and dreams public. Next generation sequencing technologies already can deliver 100-fold coverage of ten new genomes in under a week: our challenge will be to source funding and recruit the next generation of (bioinformatics-capable, genome-savvy) nematologists to drive this aspiration.

The inspirations behind the coordinated call are many-fold:

• to help ourselves: to promote cooperation between researchers sequencing nematode genomes, to share best practice, and synthetically build expertise in the whole process from DNA to annotated genome

• to attract funding: to ensure timely investment of resource in high-priority genomes, by making it evident to funding bodies that the endeavour is both likely to succeed and also has wide backing

• to coordinate efforts: to plan rationally to sequence genomes of importance to medical, veterinary, agricultural and other key areas of interest

• to cover diversity: to ensure that the full diversity of the phylum Nematoda is represented

• to foster careers: to build a growing community of genomics nematologists, or nematological genomicists, and thus enticing career paths for the researchers involved

• to sequence the uncultured: to develop the technologies required for genome sequencing from single or few specimens of environmentally sourced species.

Initially we intend to present these ideas to research conferences this summer, including the C. elegans / nematode evolution meeting at the WT Sanger Institute in June 2010. A semantic wiki website (http://1000.nematodegenomes.org/) is in preparation, and will like the arthropod genomes site, collate information on nematodes being or under consideration for sequencing, and of individuals with interests in nematode genomics.

We invite you to join this initiative. Please email back to me (mark.blaxter@ed.ac.uk) with comments and criticisms. Please pass this note on to others who might (or should) be interested. If you would like to be coauthor on the C. elegans meeting poster presentation please do say so.

Mark Blaxter

with Philipp Schiffer (Koln), Sujai Kumar (Edinburgh)

  • Why 959 nematode genomes?

All adult female hermaphrodite C. elegans have 959 somatic cells. The definition of the embryonic lineage of C. elegans from fertilised zygote to fertile adult was a milestone in C. elegans developmental biology. Just as the tree of the C. elegans embryonic lineage was a key underpinning of later work on this model nematode, we hope that a Nematoda phylogeny decorated with 959 genome-sequenced taxa will underpin the investigation of nematode biology in general. Obviously, more is always better, so 1031 genomes (the number of cells in male C. elegans) would be fine also…

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The initiative is coordinated through a collaborative wiki ( http://www.nematodes.org/nematodegenomes/ ) that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda.

Please do:

~ may all beings be happy ~

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We now have a blast server for the preliminary assemblies of the 959
nematode genomes effort at:

http://xyala.cap.ed.ac.uk/downloads/959nematodegenomes/blast/blast.php

Many thanks to:
Dave Fitch, Sandra W Clifton and WashU GSC for Caenorhabditis sp 7, 9 and 11
Asher Cutter and the GenePool for Caenorhabditis Sp 5
Marie-Anne Felix and the GenePool for Oscheius tipulae
The GenePool for Dirofilaria immitis
John Jaenike and the GenePool for Howardula aoronymphium
Simon Babayan, Judith Allen, and the GenePool for Litomosoides sigmodontis

There is some boiler plate text for each assembly specifying who the
contact person is and some information about how rough/preliminary it
is (very, in some cases!). Please do note the ‘cautionary’ information in these
comments, as these are preliminary assemblies of raw data. In particular,
if you find something VERY EXCITING, phylogenetically speaking, your
thoughts should first of all assess host contamination or food source
contamination before inferring horizontal gene transfer.

If you have been working with any genomes and would like to share them
on this blast server, please send us the assembly fasta file along
with the following information:

Assembly Name
Contact
Sequencing Centre
Assembly Version
Assembly Date
Comments

We have enough space to host a few hundred genomes, so feel
free to send multiple versions if you like. Mitochondrial and
endosymbiont genomes are welcome too, as are transcriptome
(RNASeq or EST) assemblies.

All of these assemblies are also available to download from private
urls for the nematode genomes community (i.e. they are not indexed by
search engines or open to the general public). Send me or
sujai.kumar@ed.ac.uk an email and we’ll mail you back the link to the
assembly files.

Thank you also to everyone who updated the nematodegenomes wiki.
Please let us know if you have any suggestions for changing it and
what other information you would like stored for each species. We are
planning to move all sequencing information to a strain specific page
for each species.

happy hunting
Mark Blaxter and Sujai Kumar