Table I.
tRNAs detected in the phloem exudate and codon usage frequency in pumpkin
n/a, Not analyzed.
| tRNA (Codon) | No. of Clonesa | cDNA Clone Size in nt (tRNA Region)b | Presence in PS | Processed Form in PS (Sizes in nt) | Codon Usage Frequencyc | Probes Usedd |
|---|---|---|---|---|---|---|
| tRNA-Asp (GAC) | 57 | 30–47 (3′) | ++ | Yes (∼38) | 25.2 | 41–60 |
| tRNA-Lys (AAG) | 45 | 38–46 (3′) | ++ | Yes (∼60) | 39.2 | 36–55 |
| tRNA-Gly (GGA) | 16 | 31–41 (5′) | + | Yes (∼31/∼37) | 21.4 | 6–25 |
| tRNA-Met (AUG) | 12 | 32–45 (5′) | + | Yes (∼33/∼44/∼68) | 24.7 | 8–27/53–72 |
| tRNA-Glu (GAG) | 6 | 58–60 (3′) | + | Yes (∼58) | 39.8 | 22–41 |
| tRNA-Pro (CCA) | 4 | 38–41 (3′) | + | Yes (∼42) | 14.9 | 47–66 |
| tRNA-Ser (AGC) | 2 | 42/47 (3′) | + | None | 12.0 | 56–75 |
| tRNA-Arg (CGU) | 1 | 41 (3′) | + | None | 12.0 | 31–50 |
| tRNA-Gln (CAA) | 0 | n/a | + | Yes (∼37/∼66) | 21.2 | 31–50 |
| tRNA-Ala (GCU) | 0 | n/a | + | Yes (∼35) | 24.2 | 31–50 |
| tRNA-Asn (AAC) | 0 | n/a | + | Yes (∼40) | 27.2 | 5–24/51–70 |
| tRNA-Trp (UGG) | 0 | n/a | + | Yes (∼50) | 17.1 | 30–49 |
| tRNA-Tyr (UAC) | 0 | n/a | + | Yes (∼31/∼44/∼60) | 15.6 | 11–30 |
| tRNA-Phe (UUC) | 0 | n/a | + | Yes (∼65) | 26.3 | 11–30 |
| tRNA-Cys (UGC) | 0 | n/a | + | None | 8.1 | 31–50 |
| tRNA-Leu (CUC) | 0 | n/a | + | None | 12.8 | 31–50 |
| tRNA-His (CAC) | 0 | n/a | + | None | 12.4 | 31–50 |
| tRNA-Val (GUU) | 0 | n/a | + | None | 22.0 | 46–65 |
| tRNA-Thr (ACU) | 0 | n/a | −/+ | Yes (∼36/∼49/∼61) | 13.4 | 31–50 |
| tRNA-Ile (AUA) | 0 | n/a | + | n/a | 12.4 | 46–65 |
| tRNA-Ile (AUU) | 0 | n/a | − | None | 24.3 | 31–50 |
a
Number of clones similar to tRNA found in the PS cDNA library.
b
Length of the cloned cDNA fragment in bases.
c
Codon usage frequency in pumpkin calculated per thousand codons according to release 2007 (http://www.kazusa.or.jp/codon/).
d
Region used to probe tRNAs with oligonucleotides.