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[Arthropod] Daphnia genomics, 10 years on

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Fri Jul 7 13:45:59 EST 2017

Dear arthropod genomicists,

This would be a good time to reflect on the state of Daphnia water fleas 
for genomics, environment and evolution, 10 years after public release 
of Daphnia pulex chromosome and gene information.  Instead of doing that I
will let you know that I continue work on improving genome information 
for these species, and have a new set of genes for your interest:
  Daphnia pulex, Daphnia similoides, D. galeata and D. magna gene sets 
  from EvidentialGene methods.

Daphnia have the most complicated gene/genome information of any of the animals and
plants I've worked with (now many, spanning 25 years); complicated in their
protein coding gene complexity, as well as other parts.  It isn't
a surprise that intrigues me, and maybe also you and others, as we can learn 
much about simpler genomes from the complicated ones. 

The Daphnia pulex gene set here is reconstructed mostly from current RNA-seq sets, and
mapped onto the chromosome assembly from Mike Lynch's lab result (2017 publication). It
provides I believe a more accurate and complete gene set reconstruction, by objective
measures of homology and expression.  If any of you have interests in doing gene set
comparisons, please let me know.  I'm nearly finished improving this D. pulex set,
these genes are not yet fully public, but you can view on genome maps and blast

I've had good success recently by applying genome informatics developed to work with 
Daphnia genomics complexity, to improving gene accuracy for other animals and plants, 
recently including mosquitoes, whitefly, corn plant, arabidopsis, and others.  Other 
folks also now use EvidentialGene methods with success, for plants from crops to
trees, to insects, crustacea, mouse, and others.

-- Don Gilbert

See also http://wfleabase.org/ and  http://arthropods.eugenes.org/EvidentialGene/

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

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