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[Arthropod] EvidentialGene gene sets for Honey Bee and Deer Tick (apis and ixodes)

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Sun Jun 8 20:08:10 EST 2014

Dear Arthropodists,

Here are two newly assembled gene-omes, from mRNA-seq using EvidentialGene methods.
A caveat about honey bee and deer tick sets is I've not had time to
clean them up as nicely as if someone where paying for this work, so
there remains junk among the good quality genes. This Evigene Ixodes
gene set is notably more orthology-complete than the genome-built gene

This  Apis mellifera Evigene set also is a probably near complete gene
set.  There is a subset of about 4000 genes not mapping to amel45 genome
assembly, but that appear as bee genes by by protein orthology. Also
complex genes are well assembled, including DSCAM, and other larger,
longer multi-exon genes.

Gene lola* is notable: it has the most alternate-introns found in any
gene, just as for Nasonia jewel wasp, with 55 found alt introns spread
over 200Kb in 1kb steps (more expected, Nasonia has 180+).  If you
study bee/wasp/ant social behavior, lola alts guide brain axon growth,
remember that name:   
  El-oh-el-aye Lola, lo lo lo lo Lola
  * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218142/
These are gene-omes built without genomes, or reference-free gene sets
assembled from mRNA-seq.  As such they have different values than
genome-based gene sets, one important one is no external artifacts
confound these genes.  Any protein orthology measured has not been
influenced by gene modelling using other species (with their artifacts),
or genome assembly errors.

The promised Daphnia magna gene set is overdue, but as the problem
child of arthropod genomics, this gene-rich gene set is still giving
me problems.

See poster about these this week at Arthropod Genomics Symposium 2014,

  Accuracy and completeness of an Arthro-Tripod of gene-omes, Deer Tick,
  Honey Bee, and Water Flea, from mRNA-assembled and genome-modelled

Don Gilbert, 2014 June.

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