[Arthropod] Arthropod gene orthologs at arthropods.eugenes.org

Don Gilbert via arthropod%40net.bio.net (by gilbertd from net.bio.net)
Thu Jan 7 13:50:45 EST 2010


Dear biologists,

Find an updated orthology comparison of Arthropod genes at
http://arthropods.eugenes.org/

euGenes/Arthropods contains computed protein orthologs among 14
species: 3 mosquitoes, 3 drosophila, 2 hymenoptera, 4 other
insects, a crustacean and an arachnid.

This update (ARP2) adds Bombyx silkmoth/worm, the full release
genes of Ixodes, and updated gene sets of the other species where
available. Compared with ARP1 of 2008, this is a fuller gene
grouping. The phylogenetic tree of these orthologous genes
matches fairly well the known phylogeny (see orthologs/ section).

Gene groups can be searched by gene names, descriptions and IDs.
You can also select gene groups by presence or absence in a
species. E.g. you can list 250 putative non-insect gene groups by
setting insects to None and Other Arthropods to "1+". Likewise
find 160 insect-only gene groups.  Find genes also by BLAST,
including PSI-BLAST, of the ortholog groups.

arthropods/summaries/ has some useful comparisons
 Gene structure statistics (average gene, exon, intron sizes)
    arthropod-genestruc-table.pdf and arthropod-genestruc-hist.pdf  

 Orthology gene group over/under abundances, and missed ortho-genes found
    table.overgroups.txt
    overgroups/table.overgroups.all.txt and for each species

 EST assemblies and validation of gene models
   PASA-EST-assemblies.html

This is a preliminary release as parts still need updates, including
a better consensus annotation of these gene groups.

Some comments on these genomes:

  * Pediculus (the human parasitic body louse) has an interesting
  gene set in having single copies of most of the common insect
  orthologous gene set (more than apis, aphid, culex, or
  nasonia), but almost no paralogs.  If one wanted an example of
  the basic / primordial insect gene set, Pediculus would be a
  good choice (maybe along with Tribolium).

  * Aphid and Daphnia have 4 times the number of gene
  duplications (paralogs) as any of the other arthropods, as
  previously found. Of interest, Aphid and Pediculus, at opposite
  extremes in duplicates, are most closely related.
  
  * Ixodes and Bombyx gene sets have artifactually missed a
  significant number of genes. For Ixodes at least this is
  explained from a high portion of repetitive/transposon dna, a
  challenge for assembly, yeilding a fragmented genome with
  genes split across scaffolds.  This gene finding problem is
  compounded by Ixodes having mostly long introns, longer on
  average than a full coding transcript, in contrast to the
  other arthropods with mostly short introns, except for
  Bombyx (which may also have had gene finding challenges).

  
-- Don Gilbert

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



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