conserved single copy nematode genes

Model Organism: Worms Scientific Discussion
1

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

2

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).