Table III.
AS and EST clusters in eudicot dbEST
| Species | Common Name | Cultivar | Genome Sizea | AS Rateb | dbESTsc |
|---|---|---|---|---|---|
| Mbp | std | ||||
| Arabidopsis thaliana | Thale cress | ‘columbia’ | 120 | 1.9 (0.14) | 111,142 |
| ‘wassilewskija’ | 120 | 2.7 (0.23) | 49,667 | ||
| Lotus japonicus | ‘gifu b-129’ | 470 | 3.5 (0.31) | 48,654 | |
| Medicago truncatula | Barrel medic | ‘a17’ | 500 | 4.6 (0.33) | 66,752 |
| Malus domestica | Apple | ‘Royal gala’ | 750 | 4.6 (0.25) | 117,790 |
| Solanum lycopersicum | Tomato | ‘micro-tom’ | 950 | 5.7 (0.38) | 92,074 |
| ‘ta496’ | 950 | 5.6 (0.19) | 89,186 | ||
| Glycine max | Soybean | ‘williams’ | 1,200 | 6.0 (0.44) | 91,691 |
| ‘williams82’ | 1,200 | 5.2 (0.26) | 80,218 | ||
| Lactuca sativa | Lettuce | ‘salinas’ | 2,597 | 6.9 (0.3) | 80,144 |
Data for 1C value of genome size were obtained from Plant DNA C-values Database release 5.0, December, 2004 (http://www.kew.org/cvalues/CvalServlet?querytype=2) and, where possible, from direct sequencing results from NCBI Entrez Genome Project database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj).
Selections of 20,000 EST were done in six random passes and were matched against each other. The alignment results were parsed for AS pairs and clusters and the AS rate was computed as described in the “Materials and Methods.” The complete list appears in Supplemental Table S3. The average AS rate and sd are shown here.
dbEST indicates the number of ESTs greater than 100 bp size, after removal of poly A and vector contamination, from a specific cultivar. The cultivar used was in all cases the cultivar that provided at least 40,000 ESTs.