Table 1 In-silico analysis of whole genome sequences from 9 eukaryotic species ( Homo sapiens, Oryza sativa , Anopheles gambiae , Drosophila melanogaster , Arabidopsis thaliana , Caenorhabditis elegans , Plasmodium falciparum , Schizosaccharomyces pombe and Saccharomyces cerevisiae )
From: Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species
Homo | Oryza | Anoph. | Droso. | Arab. | Caeno. | Plasm. | Schizo. | Sacch. | |
|---|---|---|---|---|---|---|---|---|---|
Genome size (Mb) | 3003 | 382 | 230 | 120 | 119 | 100 | 23 | 13 | 12 |
GC% (gene sequences) | 0.419 | 0.446 | 0.473 | 0.437 | 0.393 | 0.364 | 0.227 | 0.388 | 0.396 |
GC% (intergenic sequences) | 0.402 | 0.432 | 0.433 | 0.403 | 0.313 | 0.341 | 0.144 | 0.345 | 0.347 |
Number of genes | 36036 | 30295 | 12688 | 14604 | 33239 | 21175 | 5509 | 5060 | 6281 |
Mean (stand. dev.) gene length (kb) | 35.5 (81.2) | 3.0 (2.6) | 5.9 (4.5) | 6.3 (4.7) | 2.1 (1.6) | 2.9 (3.3) | 2.5 (2.6) | 1.4 (0.7) | 1.4 (1.2) |
Enzymes Eco RI/ Mse I | |||||||||
Number of AFLPs | 459944 | 50437 | 28336 | 20767 | 22836 | 27345 | 2017 | 2748 | 2891 |
Mean distance between AFLPs (kb) | 6.7 | 7.4 | 8.0 | 5.7 | 5.1 | 3.5 | 11.2 | 4.4 | 4.1 |
% AFLPs at a given distance from genes | |||||||||
0 kb (EXP*) | 41 (43) | 29 (25) | 28 (32) | 63 (63) | 67 (59) | 65 (59) | 79 (59) | 71 (60) | 87 (73) |
1 kb | 43 | 42 | 36 | 71 | 89 | 83 | 96 | 94 | 99 |
10 kb | 53 | 80 | 64 | 92 | 99 | 100 | 100 | 99 | 100 |
% Genes with AFLPs at a given distance | |||||||||
0 kb (EXP**) | 48 (99) | 33 (38) | 27 (46) | 35 (59) | 34 (37) | 47 (57) | 23 (25) | 31 (32) | 31 (33) |
1 kb | 63 | 50 | 45 | 56 | 55 | 70 | 31 | 56 | 57 |
10 kb | 92 | 95 | 93 | 96 | 98 | 100 | 85 | 100 | 99 |
Enzymes Bsm I/ Taq I | |||||||||
Number of AFLPs | 101630 | 31357 | 35330 | 21155 | 10441 | 12518 | 464 | 1751 | 1475 |
% AFLPs at 0 kb from genes | 45 | 30 | 33 | 64 | 73 | 69 | 92 | 76 | 84 |
Enzymes Sac I/ Hpa II | |||||||||
Number of AFLPs | 131756 | 45330 | 17529 | 10234 | 6579 | 7098 | 19 | 406 | 467 |
% AFLPs at 0 kb from genes | 52 | 29 | 39 | 72 | 86 | 75 | 100 | 89 | 87 |