[Arthropod] Recent Arthropod Transcriptome Assemblies at arthropods.eugenes.org/EvidentialGene/

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Fri Dec 7 14:06:25 EST 2012


Dear arthropod biologists,

Find a summary gene sets of animals and plants here, those developed
in the EvidentialGene project, and related reference or new species
gene sets for comparison:
   http://arthropods.eugenes.org/EvidentialGene/

As part of this project, I've  reassembled transcripomes of a few
interesting arthropods from public RNA-seq data, using methods of
EvidentialGene.  Protein and transcript sequences are available for
these, in rough form. They are not yet annotated with protein
functions.  These transcriptomes appear to be about as complete as the
genome-based arthropod gene sets, and may be of interest to some of
you:

locust, Locusta migratoria
  EvidentialGene/locust/bestof5/  locust1best5.aa.gz (proteins),
    locust1best5.tr.gz (transcripts)
  this gene set has strong orthology to many insects, possibly better general insect match
  than tribolium or hymenoptera.
  
whitefly, Bemisia tabaci
  EvidentialGene/whitefly/ whitefly1best3vel_cd90.aa.gz (proteins), 
      whitefly1best3vel_cd90.tr.gz (transcripts)
  this genes in this set look fairly complete, orthology is strong to other insects.
  
whiteshrimp,  Litopenaeus vannamei    
  EvidentialGene/whiteshrimp/ whiteshrimp1best.aa.gz (proteins), 
      whiteshrimp1best.tr.gz (transcripts)
  this is may be a 2nd crustacean gene set of quality (counting 2 daphnia species as
  still best crustacean gene set)

Gene IDs in these data are the working output of assembly process, and shouldn't be taken
as long-term IDs.

Also find here public gene sets for Nasonia wasp v2, Pea aphid v2.  The Cacao tree
gene set will be published soon.  Killifish and Daphnia magna gene sets are
still in progress, limited to genome project members.

-- Don Gilbert



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