Table 3.
Genomes and gene annotations used as references for the assessment of gene prediction accuracy.
| Species | Genome length (Mb) | Reference annotation statistics | |||||
|---|---|---|---|---|---|---|---|
| # coding genes | # coding transcripts | introns per gene | |||||
| C. elegans (roundworm) | 100 | 19,969 | 28,544 | 4.8 | |||
| A. thaliana (thale cress) | 119 | 27,445 | 40,827 | 4.0 | |||
| D. melanogaster (fruit fly) | 138 | 13,951 | 22,395 | 2.8 | |||
| S. lycopersicum (tomato) | 807 | 25,158 | (15,138) | 31,911 | (15,150) | 4.4 | (4.3) |
| D. rerio (zebrafish) | 1,345 | 25,610 | (17,893) | 42,929 | (19,975) | 8.4 | (8.4) |
| G. gallus (chicken) | 1,050 | 17,279 | (10,736) | 38,534 | (12,733) | 9.0 | (9.2) |
| M. musculus (mouse) | 2,723 | 22,405 | (16,531) | 58,318 | (20,708) | 6.0 | (8.6) |
The numbers in parentheses provided for the four large genomes characterize sets of genes and transcripts in the intersection of NCBI and Ensembl annotations (see Methods). The numbers of introns per gene were computed from averages for each gene among annotated alternative transcripts. Alternative transcripts that differ only by UTR regions are not considered.