An improved codon usage table for Phytophthora infestans
Sophien Kamoun and Allison Styer
Department of Plant Pathology,
The Ohio State University, Ohio Agricultural and Research Development Center, Wooster, OH 44691
Table 1. A codon usage table for Phytophthora infestans based on an unpublished set of 50 open reading frames (16,728 codons and 50,184 bp).
------------------------------------------------------------------------ TTT 5.4( 90) TCT 6.9( 116) TAT 5.9( 99) TGT 3.3( 56) TTC 27.1( 453) TCC 12.2( 204) TAC 31.0( 519) TGC 13.2( 220) TTA 0.9( 15) TCA 2.6( 44) TAA 2.0( 33) TGA 0.7( 11) TTG 6.9( 116) TCG 23.3( 390) TAG 0.8( 14) TGG 9.2( 154) CTT 9.9( 166) CCT 9.8( 164) CAT 2.6( 44) CGT 16.3( 273) CTC 17.5( 293) CCC 13.2( 221) CAC 13.7( 229) CGC 17.8( 297) CTA 3.4( 57) CCA 5.9( 98) CAA 4.7( 79) CGA 2.5( 41) CTG 35.8( 598) CCG 19.6( 327) CAG 26.5( 444) CGG 1.9( 32) ATT 14.7( 245) ACT 13.6( 228) AAT 5.1( 85) AGT 4.1( 69) ATC 34.7( 581) ACC 18.8( 482) AAC 31.5( 527) AGC 13.1( 219) ATA 0.8( 14) ACA 6.7( 112) AAA 5.7( 96) AGA 1.0( 17) ATG 24.0( 401) ACG 36.6( 608) AAG 51.1( 854) AGG 0.8( 13) GTT 6.9( 116) GCT 25.6( 428) GAT 11.1( 186) GGT 22.7( 379) GTC 20.2( 337) GCC 44.5( 744) GAC 46.3( 775) GGC 43.9( 734) GTA 3.8( 63) GCA 7.1( 119) GAA 16.6( 278) GGA 10.2( 171) GTG 40.9( 684) GCG 16.4( 274) GAG 56.7( 949) GGG 2.6( 43) ------------------------------------------------------------------------
Coding GC 59.1% , 1st position GC 57.6%, 2nd position GC 43.6%, 3rd position GC 76.1%
Table 2. Codon frequency in Phytophthora infestans based on an unpublished set of 50 open reading frames (16,728 codons and 50,184 bp). Over-represented codons are shown in red.
|
Codon |
Amino acid |
Number |
/1000 |
Fraction |
|
TTT |
Phe |
90 |
5.38 |
0.17 |
|
TTC |
Phe |
453 |
27.08 |
0.83 |
|
TTA |
Leu |
15 |
0.90 |
0.01 |
|
TTG |
Leu |
116 |
6.93 |
0.09 |
|
CTT |
Leu |
166 |
9.92 |
0.13 |
|
CTC |
Leu |
293 |
17.52 |
0.24 |
|
CTA |
Leu |
57 |
3.41 |
0.05 |
|
CTG |
Leu |
598 |
35.75 |
0.48 |
|
ATT |
Ile |
245 |
14.65 |
0.29 |
|
ATC |
Ile |
581 |
34.73 |
0.69 |
|
ATA |
Ile |
14 |
0.84 |
0.02 |
|
ATG |
Met |
401 |
23.97 |
1 |
|
GTT |
Val |
116 |
6.93 |
0.10 |
|
GTC |
Val |
337 |
20.15 |
0.28 |
|
GTA |
Val |
63 |
3.77 |
0.05 |
|
GTG |
Val |
684 |
40.89 |
0.57 |
|
TCT |
Ser |
116 |
6.93 |
0.11 |
|
TCC |
Ser |
204 |
12.20 |
0.20 |
|
TCA |
Ser |
44 |
2.63 |
0.04 |
|
TCG |
Ser |
390 |
23.31 |
0.37 |
|
CCT |
Pro |
164 |
9.80 |
0.20 |
|
CCC |
Pro |
221 |
13.21 |
0.27 |
|
CCA |
Pro |
98 |
5.86 |
0.12 |
|
CCG |
Pro |
327 |
19.55 |
0.40 |
|
ACT |
Thr |
228 |
13.63 |
0.16 |
|
ACC |
Thr |
482 |
28.81 |
0.34 |
|
ACA |
Thr |
112 |
6.70 |
0.08 |
|
ACG |
Thr |
608 |
36.35 |
0.42 |
|
GCT |
Ala |
428 |
25.59 |
0.27 |
|
GCC |
Ala |
744 |
44.48 |
0.48 |
|
GCA |
Ala |
119 |
7.11 |
0.08 |
|
GCG |
Ala |
274 |
16.38 |
0.18 |
|
TAT |
Tyr |
99 |
5.92 |
0.16 |
|
TAC |
Tyr |
519 |
31.03 |
0.84 |
|
TAA |
End |
33 |
1.97 |
0.57 |
|
TAG |
End |
14 |
0.84 |
0.24 |
|
CAT |
His |
44 |
2.63 |
0.16 |
|
CAC |
His |
229 |
13.69 |
0.84 |
|
CAA |
Gln |
79 |
4.72 |
0.15 |
|
CAG |
Gln |
444 |
26.54 |
0.85 |
|
AAT |
Asn |
85 |
5.08 |
0.14 |
|
AAC |
Asn |
527 |
31.50 |
0.86 |
|
AAA |
Lys |
96 |
5.74 |
0.10 |
|
AAG |
Lys |
854 |
51.052 |
0.90 |
|
GAT |
Asp |
186 |
11.12 |
0.19 |
|
GAC |
Asp |
775 |
46.33 |
0.81 |
|
GAA |
Glu |
278 |
16.62 |
0.23 |
|
GAG |
Glu |
949 |
56.73 |
0.77 |
|
TGT |
Cys |
56 |
3.34 |
0.20 |
|
TGC |
Cys |
220 |
13.15 |
0.80 |
|
TGA |
End |
11 |
0.66 |
0.19 |
|
TGG |
Trp |
154 |
9.21 |
1 |
|
CGT |
Arg |
273 |
16.32 |
0.41 |
|
CGC |
Arg |
297 |
17.75 |
0.44 |
|
CGA |
Arg |
41 |
2.45 |
0.06 |
|
CGG |
Arg |
32 |
1.91 |
0.05 |
|
AGT |
Ser |
69 |
4.12 |
0.07 |
|
AGC |
Ser |
219 |
13.09 |
0.21 |
|
AGA |
Arg |
17 |
1.02 |
0.03 |
|
AGG |
Arg |
13 |
0.78 |
0.02 |
|
GGT |
Gly |
379 |
22.66 |
0.29 |
|
GGC |
Gly |
734 |
43.88 |
0.55 |
|
GGA |
Gly |
171 |
10.22 |
0.13 |
|
GGG |
Gly |
43 |
2.57 |
0.03 |
|
total |
16728 |
1000 |
------------------------------------------------------------------------
Figure 1. Correlation of the G + C content between the examined ORFs and the first, second, and third codon positions.
Please cite:
Kamoun, S. and Styer, A. 2000. An improved codon usage table for Phytophthora infestans. http://www.oardc.ohio-state.edu/phytophthora/codon.htm
Last modified: June 1, 2000