From luisa.orsini from bio.kuleuven.be Tue Jan 5 08:33:58 2010 From: luisa.orsini from bio.kuleuven.be (Luisa Orsini) Date: Tue Jan 5 08:36:13 2010 Subject: [Arthropod] DGC conference-last call for registration Message-ID: <4B433FC6.50708@bio.kuleuven.be> Can you please post the last call for our upcoming conference? regards, Luisa Daphnia Genomics Consortium (DGC) Meeting 2010 When: 26th through 30th of March, 2010 Where: Leuven, Belgium Deadline for registration and abstract submission is 15th of January! http://bio.kuleuven.be/DGCmeeting2010.html !!!!!!note the updated list of our keynote speakers!!!! Visit our website for the latest updates on the conference Dear colleagues and friends, We are pleased to invite you to the DGC Meeting 2010. The Daphnia Genomics Consortium (DGC) is an international network of scientists with a common goal to foster the freshwater crustacean Daphnia as a premier model system for genomics in ecology, evolution and the environmental sciences. This meeting aims to bring together the members of the consortium at large, to facilitate the exchange of information on recent developments and results obtained from the ongoing investigations into the genome biology of Daphnia. Additionally, we welcome researchers working with Daphnia who are not yet DGC participants and researchers working with other model or non-model organisms in the field of ecological genomics. The DGC meeting will have a significant impact on the future development of the research groups involved in the consortium. By this time, we will have finalized our initial investigations of the draft D. pulex genome sequence, and we will begin the work of exploring data obtained from the D. magna genome sequencing project. This upcoming meeting continues the tradition of also promoting collaborations between researchers working within related disciplines, including limnology, ecotoxicology, quantitative and population genetics, systematics, molecular biology and evolution, developmental biology, genomics and bioinformatics. The meeting will have plenary lectures from keynote speakers in several research fields related to Daphnia and other model organisms. Our keynote speakers are: John Colbourne (Indiana University ) Donald Gilbert (Indiana University) Joseph Shaw (Indiana University) Dieter Ebert (Universit?t Basel) Amanda Callaghan (University of Reading) Michael Pfrender (University of Notre Dame) Christian Laforsch (Ludwig-Maximilians Universit?t M?nchen) Jean-Christophe Simon(Inra France) Denis Tagu (Inra France) Abraham Tucker (Indiana University) Kelley Thomas ( University of New Hampshire) John Manak (The University of Iowa) Ralph Pirow (University of M?nster) The symposia of our meeting will touch on several research topics: * Ecology and Evolutionary Genomics * Toxicology and Environmental Genomics of Natural and Human Stressors * Genotype by Environment Interactions * Comparative Genomics and Development * Gene Expression and Gene Function Plan to also learn about the latest open source bioinformatic and high-throughput research tools, including databases, expression and genotyping microarrays, mapping panels for trait locus mapping, molecular genetic protocols and services. The venue is at the five century-old Katholieke Universiteit Leuven, in Belgium. Leuven is a beautiful medieval town that combines a rich historical patrimonium with a cheerful, flourishing city culture and a creative atmosphere for lively exchanges and debates. We look forward to welcoming you in Leuven. The local organization committee (Luc De Meester, Luisa Orsini, Ellen Decaestecker, Kevin Pauwels, Mieke Jansen, Joost Vanoverbeke) and the co-organizers Dries Knapen, Ronny Blust and Wim De Coen (University of Antwerp), Karel De Schamphelaere and Colin Janssen (University of Gent), Michael Pfrender (University of Notre Dame) and John Colbourne (Indiana University). on behalf of the committee Luisa Orsini -- *************************************************** Dr Luisa Orsini Laboratory of Aquatic Ecology and Evolutionary Biology, Katholieke Universiteit Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium Phone: +32 016323707 Fax: +32 016320771 e-mail luisa.orsini[at]bio.kuleuven.be website:http://bio.kuleuven.be/de/dea/people.php *************************************************** From gilbertd from net.bio.net Thu Jan 7 13:50:45 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Thu Jan 7 13:52:19 2010 Subject: [Arthropod] Arthropod gene orthologs at arthropods.eugenes.org Message-ID: <201001071850.o07Iojj12464@net.bio.net> Dear biologists, Find an updated orthology comparison of Arthropod genes at http://arthropods.eugenes.org/ euGenes/Arthropods contains computed protein orthologs among 14 species: 3 mosquitoes, 3 drosophila, 2 hymenoptera, 4 other insects, a crustacean and an arachnid. This update (ARP2) adds Bombyx silkmoth/worm, the full release genes of Ixodes, and updated gene sets of the other species where available. Compared with ARP1 of 2008, this is a fuller gene grouping. The phylogenetic tree of these orthologous genes matches fairly well the known phylogeny (see orthologs/ section). Gene groups can be searched by gene names, descriptions and IDs. You can also select gene groups by presence or absence in a species. E.g. you can list 250 putative non-insect gene groups by setting insects to None and Other Arthropods to "1+". Likewise find 160 insect-only gene groups. Find genes also by BLAST, including PSI-BLAST, of the ortholog groups. arthropods/summaries/ has some useful comparisons Gene structure statistics (average gene, exon, intron sizes) arthropod-genestruc-table.pdf and arthropod-genestruc-hist.pdf Orthology gene group over/under abundances, and missed ortho-genes found table.overgroups.txt overgroups/table.overgroups.all.txt and for each species EST assemblies and validation of gene models PASA-EST-assemblies.html This is a preliminary release as parts still need updates, including a better consensus annotation of these gene groups. Some comments on these genomes: * Pediculus (the human parasitic body louse) has an interesting gene set in having single copies of most of the common insect orthologous gene set (more than apis, aphid, culex, or nasonia), but almost no paralogs. If one wanted an example of the basic / primordial insect gene set, Pediculus would be a good choice (maybe along with Tribolium). * Aphid and Daphnia have 4 times the number of gene duplications (paralogs) as any of the other arthropods, as previously found. Of interest, Aphid and Pediculus, at opposite extremes in duplicates, are most closely related. * Ixodes and Bombyx gene sets have artifactually missed a significant number of genes. For Ixodes at least this is explained from a high portion of repetitive/transposon dna, a challenge for assembly, yeilding a fragmented genome with genes split across scaffolds. This gene finding problem is compounded by Ixodes having mostly long introns, longer on average than a full coding transcript, in contrast to the other arthropods with mostly short introns, except for Bombyx (which may also have had gene finding challenges). -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ From gilbertd from net.bio.net Fri Jan 15 09:25:49 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Fri Jan 15 09:26:23 2010 Subject: [Arthropod] Nasonia jewel wasp genome paper now available Message-ID: <201001151425.o0FEPn108050@net.bio.net> Dear readers, Another arthropod genome (or three) is described here, http://www.sciencemag.org/cgi/content/abstract/327/5963/343 Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species The Nasonia Genome Working Group Science 15 January 2010: Vol. 327. no. 5963, pp. 343 - 348 DOI: 10.1126/science.1178028 We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents. [PS, Science's News item on Nasonia genome is interesting, and about as long as the genome paper; there are lots of details in the genome paper supplement. -- Don ] -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ From gilbertd from net.bio.net Mon Jan 25 20:32:34 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Mon Jan 25 20:33:31 2010 Subject: [Arthropod] Another side of arthropod news Message-ID: <201001260132.o0Q1WYY19281@net.bio.net> Here if you haven't found it yet is another side to news of arthropods http://arthropoda.wordpress.com/ Michael Bok has some interesting bits on strawberry crabs, crush-staceans, tree lobsters, recent news stories where arthropods are making it big, and science highlights such as origin of insect wings. -- Don From gilbertd from net.bio.net Sun Jan 31 18:36:19 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Sun Jan 31 18:37:24 2010 Subject: [Arthropod] Daphnia has the most ancestral arthropod gene set (of those available) Message-ID: <201001312336.o0VNaJo08301@net.bio.net> Here is a factoid about Daphnia and Ixodes genes relative to insects: Daphnia has 21% of the best gene matches to human genes, Ixodes is second with 16%, with the best insect (tribolium) at 12%, and the Dipterans (drosophila, mosquitoes) trail at 3% best human gene matches. Considering other eukaroyte models (weed, worm, yeast), Daphnia remains with 21% best gene matches, but Ixodes falls to the insect level of 10%. This suggests Daphnia retains the most ancestral eukaryotic genes. This comes from blast-matching human and 5 other model gene sets from Swissprot to 14 arthropod gene sets. It includes 20000 human genes, 16000 mouse, 9000 weed, 7000 yeast, and 3000 worm genes. Arthropod genes are those used at http://arthropods.eugenes.org/arthropods/orthologs/ -- Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/