Acrobeles complexus

nematodes.org

Nematode & Neglected Genomics
@ The Blaxter Lab, Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh

 University of Edinburgh crest   

Nematode & Neglected Genomics

The Blaxter lab website, databases and services, version 4.0
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NEMBASE4

NEMBASE is a comprehensive Nematode Transcriptome Database
including 63 nematode species, over 600,000 ESTs and over 250,000 proteins.
November 2011
Nematode transcriptomics review
preprint available
  Bang logo    

We have written a short review and perspective on nematode transcriptomics for International Journal for Parasitology, including, inter alia an analysis of ALT genes from nematodes Open access to full text here.

Genomics and transcriptomics across the diversity of the Nematoda.
Blaxter M, Kumar S, Kaur G, Koutsovoulos G, Elsworth B.
Parasite Immunol. 2011 Nov 2. doi: 10.1111/j.1365-3024.2011.01342.x. [Epub ahead of print]
November 2011
The 959 nematodes genomes project:
publication of wiki database
preprint available
  Bang logo    

The 959 nematode genomes project is promoting the sequencing of as many genomes from Nematoda as possible to inform studies of genome evolution, gene evolution, the evolution of parasitic habits, and identify targets for intervention in major nematode diseases. Behind the initiative is a semantic media wiki, and this resource is described in a pre-publication NAR Database Issue article by Sujai Kumar, Philipp Schiffer and Mark Blaxter: Open access to full text here.

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
Sujai Kumar; Philipp H. Schiffer; Mark Blaxter
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr826
July 2011
Heligmosomoides proteome
  H. polygyrus by Constance Finney    

James Hewitson of Rick Maizels' group has just published an in-depth survey of the proteome of Heligmosomoides polygyrus, a model gut nematode. GenePool bioinformaticians assisted in this work building transcript models from Sanger and 454 data. See the paper at Journal of Proteomics: Proteomic analysis of secretory products from the model gastrointestinal nematode Heligmosomoides polygyrus reveals dominance of Venom Allergen-Like (VAL) proteins. James P. Hewitson, Yvonne Harcus, Janice Murray, Maaike van Agtmaal, Kara J. Filbey, John R. Grainger, Stephen Bridgett, Mark L. Blaxter, Peter D. Ashton, David A. Ashford, Rachel S. Curwen, R. Alan Wilson, Adam A. Dowle, Rick M. Maizels
June 2011
NEMBASE4 published
  NEMBASE4    

We are pleased to announce the publication of a paper describing, and illustrating the use of, NEMBASE4, our nematode EST analysis resource. This is a major piece of work by Ben Elsworth and colleagues. It is published as fully OPEN ACCESS in international Journal for Parasitology http://www.sciencedirect.com/science/article/pii/S0020751911001044 or doi:10.1016/j.ijpara.2011.03.009

The data underpinning the analyses have been deposited in the Dryad repository: doi:10.5061/dryad.b22430s2
June 2011
RAD sequencing review
  RAD     In collaboration with colleagues in Oregon we have published a review of RAD sequencing and other reduced representation next generation sequencing methods for genetic analyses of model and non model organisms - see Nature Reviews genetics http://www.nature.com/nrg/journal/v12/n7/full/nrg3012.html
May 2011
PartiGene version 3.0.6
http://en.wikipedia.org/wiki/Eupelmidae     PartiGene is a software suite for assembling and annotating EST datasets. We have corrected a few 'bugs', and improved the look and feel of the software. This is a maintenance release - see http://www.nematodes.org/bioinformatics/PartiGene/
May 2011
From genomes to markers
http://en.wikipedia.org/wiki/Eupelmidae     In collaboration with Konrad Lohse and Graham Stone, we have worked on developing exon-primed, intron-spanning markers from ESTs and preliminary next-generation genome 'skim' data. The paper "Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data" by Lohse K, Sharanowski B, Blaxter M, Nicholls JA, Stone GN is in Molecular Ecology Resources : Mol Ecol Resour. 2011 May;11(3):521-9. doi: 10.1111/j.1755-0998.2010.02956.x. Epub 2010 Dec 20.
May 2011
jMOTU and Taxonerator for DNA barcode analyses
jMOTU splash     One way of prospecting for new species is to use DNA barcoding technologies to sample target loci, and to count the numbers and diversity of molecular operational taxonomic units (MOTU) found. jMOTU is a java-based software tool for the analysis of large DNA barcode datasets. In conjunction with its companion tool Taxonerator, it facilitates the analyses of Roche 454 and Sanger-sequenced data, adding taxonomic identifiers to identified sequence clusters. Martin Jones, Anisah Goorah and Mark Blaxter. 2011 jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units. PLoS ONE 6(4): e19259. doi:10.1371/journal.pone.0019259
May 2011
Plutella xylostella genetic map using RAD
Plutella xylostella from http://www2.nrm.se/en/svenska_fjarilar/p/plutella_xylostella.html     Insecticide resistance in the diamondback moth pest Plutella xylostella is of major importance. In collaboration with Simon Baxter (Cambridge) we have used RAD sequencing to produce a linkage map for this species. This is (one of) the first time(s) RAD has been used in a non-model species to generate such global data. See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019315
April 2011
The worms' turn
Anatomy of C. elegans by Mark Blaxter     Caenorhabditis elegans is one of the foremost research organisms. In this PLoS Biology essay Mark Blaxter places C. elegans in its evolutionary and biological context. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001050
April 2011
Velvet Worms
velvet worms by Paul Sunnucks   Velvet Worms, or Onychophora, are fascinating and delightful members of the Ecdysozoa. In a short review for Current Biology, Paul Sunnucks and Mark Blaxter discuss their biology, relationships, and the available genetic and genomic resources. see http://dx.doi.org/10.1016/j.cub.2011.02.017
March 2011 and earlier
OLD NEWS previous newsflashes from us...
1000 nematode genomes   the 1000 nematode genomes initiative
genomics databases   genomic and transcriptomic databases for nematodes and other metazoan phyla
software tools   freely downloadable tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics
research projects   the work we do on the genomics, evolution and diversity of animals
CIIE   The Blaxter lab is part of the Centre for Infection Immunity and Evolution of the University of Edinburgh
GenePool   The GenePool Genomics Facility and the NERC NBAF sequencing facility

The website is continuously "under reconstruction" - please email mark.blaxter-at-ed.ac.uk if you find a significant broken link.

BaNG website, version 4.01, May 1st 2010
Website Highlight

Blaxter Lab Publications 2006
wolbachia

What do Wolbachia do for filarial nematodes?

A short review discussing the roles that Wolbachia may play in the lifestyles of filarial nematodes, based on the complete genome sequence of Brugia malayi Wolbachia

Fenn K, Blaxter M. Wolbachia genomes: revealing the biology of parasitism and mutualism. Trends Parasitol. 2006 Feb;22(2):60-5. doi:10.1016/j.pt.2005.12.012 .

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