From scott.cornman from gmail.com Tue Jun 1 12:57:46 2010 From: scott.cornman from gmail.com (scott cornman) Date: Tue Jun 1 13:29:44 2010 Subject: [Arthropod] Re: Arthropod Digest, Vol 7, Issue 1 In-Reply-To: <201006011703.o51H39d04527@net.bio.net> References: <201006011703.o51H39d04527@net.bio.net> Message-ID: Hi Don, Is one of your groups the Osiris gene cluster (so named in Drosophila)? We are starting some exploratory work on that gene family because six members were up-regulated in one of our experiments. We've noted a remarkably strong one-to-one conservation with Drosophila for a gene family of that size (~20 members), but haven't yet checked the other arthropod genomes. Although of unknown function, that gene cluster is notable for underlying a haploid and triploid lethal locus in Drosophila (DR Dorer, JA Rudnick, EN Moriyama, AC … - Genetics, 2003), it would be interesting to see how the haplodiploid species differ in that regard (presumably they must differ!). Scott Cornman Bee Research Lab USDA-ARS, Beltsville, MD On Tue, Jun 1, 2010 at 1:03 PM, wrote: > Send Arthropod mailing list submissions to >        arthropod@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit >        http://www.bio.net/biomail/listinfo/arthropod > or, via email, send a message with subject or body 'help' to >        arthropod-request@net.bio.net > > You can reach the person managing the list at >        arthropod-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Arthropod digest..." > > > Today's Topics: > >   1. Six ancient arthropod gene groupings: who would like to >      describe them? (Don Gilbert) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 31 May 2010 17:38:16 -0500 > From: Don Gilbert > Subject: [Arthropod] Six ancient arthropod gene groupings: who would >        like to describe them? > To: bionet-biology-vectors@moderators.isc.org > Message-ID: > > I've located 6 sets of ancient conserved gene groupings, in > daphnia thru diptera.  Is there someone who would like to write > these into a paper, adding some biology? > > These are two or more genes that are next to each other in > Daphnia and 5 or 4 insects (aphid, pediculus, nasonia, > drosmel/drosmoj, anopheles). Some of these may have been found as > paired before, but I can't find reports for others.   Some are > duplicates, others appear to be 2 different genes, and one case > looks like 3 different genes.  One case may have conserved > non-coding expression between paired coding genes.  These are > drawn from data of http://arthropods.eugenes.org/ > > -- Don Gilbert > > > > ------------------------------ > > _______________________________________________ > Arthropod mailing list > Arthropod@net.bio.net > http://www.bio.net/biomail/listinfo/arthropod > > > End of Arthropod Digest, Vol 7, Issue 1 > *************************************** > From gilbertd from cricket.bio.indiana.edu Tue Jun 1 14:44:49 2010 From: gilbertd from cricket.bio.indiana.edu (Don Gilbert) Date: Tue Jun 1 14:46:14 2010 Subject: [Arthropod] Re: Arthropod Digest, Vol 7, Issue 1 Message-ID: <201006011944.o51Jins14758@cricket.bio.indiana.edu> Scott, > Is one of your groups the Osiris gene cluster No, this one isn't in my short list. Osiris looks like it is a gene set limited to insects; as I required Daphnia to be part of the groups, it was left out. The same computational methods could be applied to finding insect-specific conserved groupings. This paper started me looking, with this observation: "In vertebrates, gene organisation and synteny is often conserved over long evolutionary distances... In arthropods few such complexes exist." Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of Split Complex Elizabeth J Duncan and Peter K Dearden doi: 10.1101/gr.104794.109 Given what I found, it is seems accurate that few exist across arthropods, but also there remain some yet to be found. The methods I used preclude finding all conserved gene groupings, based on having adjacent ordered genes for 6 species that also have reciprocal best matches to that same ortholog in the other species. Cases where genes diverged enough to drop out of best match status, but retained their ordered grouping are not included. Also given the draft nature of some of these genomes, several orthologous genes have yet to be well defined. This "Enhancer of Split Complex" is one such case, where the Daphnia gene models are not fully accurate. - Don From gilbertd from net.bio.net Thu Jun 24 08:54:01 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Thu Jun 24 08:55:14 2010 Subject: [Arthropod] Pediculus humanus louse genome paper is available Message-ID: <201006241354.o5ODs1h16594@net.bio.net> Dear all, The genome paper for the louse Pediculus humanus is available, This insect has the smallest number of genes yet for an arthropod. It has however a "complete" gene set; its extras have been lost. Find at http://www.pnas.org/cgi/doi/10.1073/pnas.1003379107 Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. - 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 Jun 25 15:54:31 2010 From: gilbertd from net.bio.net (Don Gilbert) Date: Fri Jun 25 15:56:16 2010 Subject: [Arthropod] More aphid gene duplicates, for insecticide resistance Message-ID: <201006252054.o5PKsVH20690@net.bio.net> Here is a new report of new gene duplications in an Aphid, which seems to grow new genes easily where needed, for insecticide resistance in this case, http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000999 in contrast to the body louse we just learned of, that lives by sucking up our blood with a minimal gene set. This makes me wonder just how labile the eukaryote genomes we have studied are? Notice the lab-rat of insect world, Drosophila mel, has the smallest gene set next to body louse (and apparently smallest among 12 drosophila). Is this, in part, from genes lost during this Dmel's salad decades of life in the lab bottles of Morgan, Sturtevant, Muller and friends? -- Don -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu--http://marmot.bio.indiana.edu/ From gilbertd from indiana.edu Sat Jun 26 13:50:52 2010 From: gilbertd from indiana.edu (don gilbert) Date: Sat Jun 26 13:55:30 2010 Subject: [Arthropod] Re: Six ancient arthropod gene groupings: who would like to describe them? Message-ID: <59128EE9-3A54-4C6E-85F7-1BC1931C56B6@indiana.edu> > I've located 6 sets of ancient conserved gene groupings, in > daphnia thru diptera. Is there someone who would like to write > these into a paper, adding some biology? > .. from data at http://arthropods.eugenes.org/ One of these 6 pairs is even more ancient, a conserved pairing from nematodes thru humans. It is known as such within the vertebrates, but so far I've not found a paper that has identified this much more ancient pairing. In all genomes, the pairing is reverse tandem (5'-5'). Expression is strongest in embryos for both genes (in drosmel, daphnia, and worm), dropping off in adults. Does this whet anyone's appetite to help write a simple paper? Of the other 5, one may be conserved outside arthropods, but not as broadly. A few others are not apparently conserved grouping outside arthropods, but one pair seems to have one ortholog in nematodes, the other's best match is in humans with no obvious nematode ortholog. - Don -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd@indiana.edu -- http://marmot.bio.indiana.edu/