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
Please use the navigation bars above to tour this site

OLD NEWS:

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
Tuberculosis drug resistance
This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #4428.     In collaboration with Nigel Saunders, we have used genome re-sequencing to address the mutational processes that occur during the evolution of drug resistance in Mycobacterium tuberculosis during a clinical infection, and identified mutations underpinning incremental acquisition of the multigrug resistance phenotype. See Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background
January 2011
Review of a RAD-ical technology
RAD tags. Image by John Davey     Restriction Site-Associated DNA sequencing (RAD-Seq) is a novel application of next generation technologies that offers the prospect of high-resolution genetic analysis in any species. John Davey, a postdoc in the Blaxter lab, has published a short review of the technology and its promise in Briefings in Functional Genomics (2010) 9 (5-6): 416-423. doi: 10.1093/bfgp/elq031 . See the UK RAD sequencing wiki for more information on applications of this technology https://www.wiki.ed.ac.uk/display/RADSequencing/Home
January 2011
iPhy - a phylogenomics workbench
the iPhy logo by Martin Jones     iPhy is a phylogenomics workbench that simplifies the tasks of collecting, verifiying and analysing multigene datasets for phylogenetic analysis. iPhy has been developed by Martin Jones, a postdoc in the Blaxter Lab. The paper is available as a preprint from BMC Bioinformatics at http://www.biomedcentral.com/1471-2105/12/30. iPhy is available here. See also the LabTimes article discussing iphy at http://www.lab-times.org/labtimes/issues/lt2011/lt03/lt_2011_03_48_49.pdf
December 2010
The Dark Matter of the Genome
Science image   Mark Blaxter wrote a perspective for Science to accompany the publication of the ModENCODE papers from the Drosophila melanogaster and Caenorhabditis elegans teams. See http://www.sciencemag.org/content/330/6012/1758.full.
October 2010
Marine metazoan biodiversity In collaboration with Si Creer and colleagues we used 454 sequencing to unmask putatively diverse marine metazoan biodiversity in a Scottish temperate benthic ecosystem. We show that remarkable differences in diversity occurred at microgeographical scales and refute currently accepted ecological and taxonomic paradigms of meiofaunal identity, rank abundance and concomitant understanding of trophic dynamics. Nat Commun. 2010 Oct 19;1:98. doi: 10.1038/ncomms1095.
October 2010
Optimising assembly of 454 transcriptome data Our paper on optimising transcriptome assemblies from Roche 454 data has been published: "Comparing de novo assemblers for 454 transcriptome data" Sujai Kumar and Mark L Blaxter BMC Genomics 2010, 11:571doi:10.1186/1471-2164-11-571 [see here for how to get Newbler 2.5].
September 2010:
Malaria drug resistance Our work in collaboration with Paul Hunt on the genetic basis of drug resistance in the malaria parasite Plasmodium chabaudi has been published in BMC Genomics 2010, 11:499 doi:10.1186/1471-2164-11-499 .
August 2010:
Ecdysozoan Mitogenomics Our work in collaboration with Omar Rota-Stabelli on the mitochondrion of the tardigrade Hypsibius dujardini and other ecdysozoa, entitled "Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda" has been published in GBE .
August 2010:
H. polygyrus genome BLAST The first draft assembly of the genome of Heligmosomoides polygyrus (Rick Maizels lab strain) from GenePool is available on the nematodegenomes BLAST server
July 2010:
1000 Nematode Genomes BLAST server We have generated a BLAST server for the preliminary data emerging from the 1000 nematode genomes collaboration.
July 2010:
Dr Pablo Fuentes-Utrillo: New research fellow Dr Pablo Fuentes-Utrillo has been awarded a two year fellowship from the Spanish Government to work with the Blaxter lab and the GenePool on RAD sequencing for forest trees.
July 2010:
RAD sequencing grant awarded We have been awarded a one-year grant from NERC (with Per Smiseth, IEB) to develop the RAD sequencing method further for NERC area science, focussing on three pilot projects on oaks, Nicrophorus beetles and C. elegans.
June 2010:
Heliconius pattern formation grant success In collaboration with Chris Jiggins (Cambridge) and Richard ffrench-Constant (Exeter) we have been awarded a BBSRC grant to study the genetics of pattern formation in Heliconius butterflies.
June 2010:
 RAD sequencing grant success In collaboration with Matt Hegarty and Justin Pachebat (Aberystwyth), we have been awarded a BBSRC grant to apply RAD analysis to plants
June 2010:
 HiSeq delivered to GenePool The GenePool, the University of Edinburgh Genomics Facility has received delivery of the new Illumina HiSeq 2000 200-Gbase-per-run instrument
June 2010:
 jMOTU and Taxonerator released jMOTU and Taxonerator, java tools for the analysis of DNA barcode data from Sanger and 454 sequencing have been released jMOTU and Taxonerator are written by Martin Jones and Anisah Ghoorah
June 2010:
 prot4EST New Version The EST to protein translation suite version 3.0b released on 21 June 2010 DOWNLOAD from compsysbio.org prot4EST is written by James Wasmuth
May 2010:
1000 Nematode Genomes Launched Join the 1000 nematode genomes project, propose species for sequencing, and review progress here

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
evolution of operons

The evolution of Wolbachia

By sequencing ~8% of the genome of the Wolbachia endosymbiont of Onchocerca volvulus we have estimated the phylogentic history of this important group of symbionts.

Fenn K, Conlon C, Jones M, Quail MA, Holroyd NE, Parkhill J, Blaxter M. Phylogenetic relationships of the Wolbachia of nematodes and arthropods. PLoS Pathog. 2006 Oct;2(10):e94. DOI: 10.1371/journal.ppat.0020094 .

[nematodes.org v4.0] the content of these pages is copyright Mark Blaxter and colleagues. Contact the webmaster if there are problems.