conserved single copy nematode genes

to collect some resources and comments on creating sets of conserved single copy nematode genes.

published sets:

Mitrieva, et. al, “The draft genome of the parasitic nematode Trichinella spiralis”. Nat Genet, 43, 228-35. (WBPaper00038148)
contains 328 protein families represented by a single copy gene in all six species (C.elegans, B.malayi, M.incognita, T.spiralis, D.melanogaster, S.cerevisiae), 85 nematode specific.

Genis Para, et. al, “Assessing the gene space in draft genomes”,Nucleic Acids Res. , 2009 January; 37(1): 289–297
contains 248 protein families (based on KOG) consisting of single copy genes from H.sapiens, D.melanogaster, A. thaliana, C. elegans, S. cerevisiae and S.pombe

comments based on efforts by WormBase, the Blaxter lab and the Schwarz lab to come up with a more comprehensive and nematode specific set:

  • many draft genomes contain quite a bit of heterozygosity
  • rough gene predictions can miss or mispredict loci
  • paralogs and pseudogenes can cause “duplications”

Hermaphrodite species, like C.briggsae, C.elegans, P.pacificus or C.sp 11 seem to be a good source. (with the caveat that the C. sp 11 genome and gene set is still in draft form).