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.
http://arthropods.eugenes.org/EvidentialGene/daphnia/
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
searches.
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/
