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Index of /genome-summaries/gene-homology

      Name                            Last modified       Size  Description

[DIR] Parent Directory 30-Mar-2008 14:08 - [TXT] daphnia-bestmod.txt 13-Mar-2007 18:36 2k [TXT] daphnia-foundgenes-aug06.html 04-Feb-2007 15:49 16k [DIR] daphnia-foundgenes-aug06_files/ 04-Feb-2007 15:43 - [   ] daphnia-foundgenes-aug06.pdf 04-Feb-2007 15:01 75k [   ] daphnia-foundgenes-aug06.ppt 04-Feb-2007 14:41 113k [TXT] genome-mean-dmelgene.html 26-Jul-2006 13:10 2k [IMG] genome-mean-dmelgene.png 20-Apr-2006 21:11 15k [   ] genome-mean-dmelgene.pdf 20-Apr-2006 21:07 47k

Eukaryote Gene homology for Daphnia and Drosophila genomes

Eukaryote Gene homology for Daphnia and Drosophila genomes

Genes Found in new Genomes
Figure 2. Percent of full gene sets of nine reference eukaryote genomes found in new genomes Daphnia pulex, Drosophila mojavensis, and reference genome Anopheles gambiae, from DroSpeGe and wFleaBase genome analyses. The lower section shows total number of protein genes for each reference genome, with the upper section the percent of these found in new genomes. New genome D. mojavensis has 90% similarity to the reference fruitfly D. melanogaster, and A. gambiae has 100% similarity to itself. These are taken from tBLASTn analyses with a match significance of 1e-10 or stronger.
Genes Found Table
Species Fish Human Mouse Dmel Mosquito Bee Worm Yeast Weed Total
Dros.grimshawi 14819 12357 10440 12188 10328 6466 7018 2320 8797 84733
Dros.mojavensis 14930 12434 10481 12276 10503 6519 7071 2330 8874 85418
Daphnia 15172 12429 10522 7965 8236 6018 6453 2244 8577 77616
Mosquito 15123 12534 10551 9920 14193 6571 7032 2355 9092 87371
Total genes 23524 22216 18941 13472 14364 9671 19765 5777 28860 156590
Percent found of Total Genes in Genomes
Species Fish Human Mouse Fruitfly Mosquito Bee Worm Yeast Weed Average
Drosophila 63.47 55.97 55.33 91.12 73.12 67.41 35.78 40.33 30.75 47.13
Daphnia 64.50 55.95 55.55 59.12 57.34 62.23 32.65 38.84 29.72 46.52
Mosquito 64.29 56.42 55.70 73.63 98.81 67.95 35.58 40.77 31.50 47.60
Average 64.08 56.11 55.53 74.63 76.42 65.86 34.67 39.98 30.66 47.08
Daphnia averages slightly fewer % found, excluding insects, than Dros, Mosquito. This may well be an artifact due to assembly incompleteness. However Daphnia shows 50 - 100 more Fish genes than insects (compare mammal genes). This might be eco-genetic rather than taxonomic or assembly artifact. Details of which Fish genes are in Daphnia not in insects may validate this.

Don Gilbert, August 2006