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[Arthropod] Re: Daphnia has the most ancestral genes

Jeffrey Boore via arthropod%40net.bio.net (by jlboore from calmail.berkeley.edu)
Tue Feb 2 21:40:24 EST 2010

I cannot resist an advertisement here myself.  We have a system called  
PHRINGE (Phylogenetic Resources for the Interpretation of Genomes)  
that uses a graph-based method for recognizing gene families that  
incorporates the evolutionary relationships among the organisms,  
reconstructs evolutionary trees for all genes in all considered  
genomes, and links this up with outside databases.  Users can compare  
intron-exon structures, see the tree of each set of genes, download  
the multiple sequence alignments, see the relative physical  
arrangements of orthologous genes, and do other cool stuff.

The best implementation is for oomycete genomes at <http://oomycetes-public.genomeprojectsolutions-databases.com/ 
 >.  (Click on the links and/or plug in some random gene numbers if  
you want to see how it works.)  We don't have anything yet for  
arthropods, because I have failed to convince DOE, NSF, or NIH to  
support this (rant suppressed here), but we intend to do that as part  
of our project sequencing the monarch butterfly genome.  That  
sequencing will be complete in a few months.


Jeffrey L. Boore, Ph.D.
Chief Executive Officer
Genome Project Solutions
1024 Promenade Street
Hercules, CA 94547

1 (877) 867-0146 (toll free)

Associate Adjunct Professor, University of California Berkeley
Guest Researcher, Berkeley National Lab and DOE Joint Genome Institute

On Feb 1, 2010, at 11:52 PM, Mark Blaxter wrote:

> Hi Dan
> could you get the genes into the TreeFam project also? Will the  
> ensembl genomes project be 'doing' the trees?
> Mark
> On 1 Feb 2010, at 22:28, Daniel Lawson wrote:
>> HI
>> Well this is one of the aims for the Ensembl Genomes project  
>> (excuse the blatant advertising). All of Don's model organism  
>> genomes are represented and from an arthropod point of view we are  
>> missing Daphnia, Tribolium, Nasonia, Aphid, Apis and Bombyx (so 6  
>> out of 14 species). Some of these will be incorporated during the  
>> spring so we could consider such an analysis in the summer.
>> regards
>> Dan
>> -- 
>> Ensembl Genomes | VectorBase
>> On 1 February 2010 20:59, Mark Blaxter <mark.blaxter from ed.ac.uk> wrote:
>> Hi folks
>> I'm always worried when BLAST is used as a phylogenetic tool...  
>> basically the 'scores' returned are contingent on the underlying  
>> model, which in BLAST is evolutionary/biological of course, but is  
>> generalised across all proteins. Statements of 'basal' imply a  
>> tree, and a tree implies a model driven reconstruction, and, well,  
>> BLAST doesnt reconstruct trees.
>> A top blast match (or reciprocal best blast) algorithm is severely  
>> biased by
>> - the relative rates of substitution in each genome
>>       all extant genomes are equally 'evolved'; the differences are  
>> in rates and patterns of rates of evolution across genes
>>       two genomes with relatively low substitution rates will  
>> appear more similar than expected when compared to their sister  
>> taxa, when sister taxa have elevated rates
>> - the patterns of substitution that are driven by other forces,  
>> such as base composition
>>       its well known in mitochondrial genomes that protein  
>> substitution patterns are driven by genome AT content, resulting in  
>> significant and completely confounding homoplastic convergence at  
>> the amino acid level
>>       thus global comparisons using BLAST, using a single  
>> substitution matrix (that implicitly assumes equivalence of amino  
>> acid composition bias) will mislead
>> It would be good to derive trees for all of the protein sets Don  
>> has generated and ask what their topologies are. Are these genes  
>> not in TreeFam, where there are trees derived that can be mined for  
>> data affirming this finding.
>> Mark
>> On 1 Feb 2010, at 17:40, Don Gilbert wrote:
>> Scott,
>> Yes, to be sure, I qualified it 'the most ancestral arthropod gene  
>> set (of
>>       those available)'..
>> It may be a slog thru many arthropod genomes to find "the  
>> ancestral" model;
>> from insect genomes, it is clear even the phylogenetically basal  
>> ones are
>> more derived than ixodes or daphnia, and that agrees with known  
>> phylogeny (?).  Part
>> of Ixodes lower score is its highly repetitive genome, subsequent  
>> poor assembly, and
>> artifactually poorer gene models (missing in all or parts).  But  
>> the distinction
>> in Ixodes better score to mammal genes vs plant/worm suggests a  
>> real difference
>> from Daphnia.
>> Another thing I noticed in these stats of non-arthropod homology, I  
>> can't put too much
>> weight on its biological accuracy but someone could investigate  
>> further:
>> pediculus (mammal parasite) and aphid (plant parasite) are two  
>> relatively close insects,
>> and should by phylogeny have about same gene distance from non- 
>> arthropods.  Not quite:
>> pediculus favors mammal genes over aphid by 2%, and aphid favors  
>> plant genes over
>> pediculus by 1%, the only case I looked at where aphid exceeds  
>> louse.  More details are here:
>> http://arthropods.eugenes.org/arthropods/summaries/best-arp-model6genes.txt
>> - Don
>> |Subject: Re: Daphnia has the most ancestral genes
>> |
>> |Hi Don,
>> |
>> |I thought that was an interesting comparison you posted on Arthropod
>> |Digest, but I wonder if there will be a non-parasitic arthropod  
>> genome
>> |coming out that would be a better indicator of ancestral genes (eg a
>> |spider?). Mites and ticks have a long history of parasitism and that
>> |has been shown to be associated with gene loss, I believe.
>> |
>> |Scott Cornman
>> |Beltsville Bee Research Lab
>> |
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>> -- 
>> Ensembl Genomes | VectorBase
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