daphnia genome

Comparative gene content analysis
We compared the gene content of the Daphnia genome (the FrozenGeneCatalog_2007_07_03 set) with other representative species with available complete genomes by identifying orthologous and homologous relations among the genes (orthologous groups). Of the 30,940 predicted genes almost half does not show significant homology to genes in the other species considered (in comparison, the fraction is much less for Sea urchin considering all 29,128 models while only 23,300 of them are estimated to be actual genes). List of D.pil unique genes (E-val<1e-3)

Fig_comp_orthology. daphnia orthogr dist daphnia orthogr dist2

A bit more on comparison of the Daphnia unique genes against the genes with homology support:
1. average length of the unique genes is about 200 aa while the homologous genes are about 400 aa
2. dpul genefam sizes 2dpul genefam sizes 2

based on the previous gene set Fig_comp_orthology, [data_file]).

Expansions or contractions of gene families may be indicative of functional adaptation, hence we compared the gene repertoires at the level of sizes of gene families generally defined by InterPro protein domain signatures [top500, sorted by difference] .

Case studies

  • An example of a drastic Daphnia gene expansion is Fatty acyl-CoA reductase (EC 1.2.1.-)
  • daphnia expansiondaphnia expansion
  • Another axample is expansion of orthologs of human UDP-/ UDP-galactose-ceramide glucuronosyltransferase (EC / EC (orthologous group 6331)

Repertoure of microRNAs
We predicted 40 pre-miRNA genes [GTF, Fasta] using an SVM classifier with other insect orthology evidence, 23 of which are highly similar to known animal miRNAs.
An unknown miRNA universally present in Daphnia and several insects
missing mirnamissing mirna

Dpul_mir.fas6.84 KB
Dpul_mir.gtf3.7 KB
iprs_Aedes1.1_Feb2007.raw.gz2.29 MB
iprs_Dpul_Jul2007_patched.raw.gz2.36 MB
iprs_Fly5.1_Feb2007.raw.gz2.78 MB
iprs_Nematostella_Mar2007.raw.gz3.27 MB
iprs_Tcas_curated_Mar2007.raw.gz2.1 MB
daphnia_orthologous_groups.txt4.7 MB
dpul_jan08_pubogs.txt3.31 MB
dpul_unique.txt484.52 KB
dpulnvec_jan08_pubogs.txt4.1 MB
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