[Arthropod] Arthropod genomes in progress?

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Wed Dec 9 14:08:46 EST 2009


Dear folks,

To follow up on Yannick's question about problems analyzing 
ant genes without an ant genome assembly, I also would like to learn
what arthropod genomes are now being sequenced, with some prospect 
of public data access this coming year.

I use NCBI's Genomes table of genome projects in progress, 
http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi
But smaller groups are not often signing into this, so we
now lack a good view of what genomes may be coming.  

Do any of you have pointers to other arthropod genomes in progress?
I've heard rumors of ant genomes being sequenced.  

The Daphnia genomicists are working on Daphnia magna (at around
8x cover now but not completely covering the genome), and a
postdoc is sequencing a set of Daphnia populations (pulex or
related species).

We are at the stage now where genome sequencing/assembly/analysis 
is something a postdoc or research lab does, as often or more often
than the sequencing centers.  Yet there is much effort needed to turn
sequence from machines to into a good genome assembly and analysis.
Those groups who want benefits that collaborations can bring should
let us know what is coming along.  

Often when I think I find a phylogenetic or other relationship from
available arthropod genomes, another one comes along to confuse
or disprove that.  

For example, Ixodes tick has mostly long introns like
vertebrates, unlike other bugs.  But then I looked at the silk
moth genome, and it also has a preponderance of long introns.

Find here a summary of arthropod gene structure statistics such as
exon and coding sequence sizes, intron sizes and number of exons, 
showing this bit about intron size distribution
http://insects.eugenes.org/arthropods/summaries/
arthropod-genestruc-table.pdf
(with frequency plots in arthropod-genestruc-hist.pdf)

-- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd from indiana.edu--http://marmot.bio.indiana.edu/



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