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Table 2 Effect of base composition independent of translational selection.

From: The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast

Amino acid Gene length Expression Recombination
FGCopt: Frequency of GC-ending optimal codons, n = 1506 genes
Ile
N = 47505 codons
-0.1567*** +0.1026*** Co:+0.2280***
nCo:+0.2027***
spo11:+0.2754***
dmc1:+0.3490***
mre110:+0.1663***
mre116:+0.2185***
Ser
N = 36478 codons
-0.1054*** +0.0354NS Co:+0.1602***
nCo:+0.0926***
spo11:+0.1722***
dmc1:+0.2429***
mre110:+0.1185***
mre116:+0.1602***
Thr
N = 30830 codons
-0.0899** +0.0837** Co: = 0.2019***
nCo:+0.1365***
spo11:+0.2252***
dmc1:+0.2827***
mre110:+0.0958**
mre116:+0.1302***
Val
N = 32710 codons
-0.1544*** +0.0954*** Co:+0.2036***
nCo:+0.1433***
spo11:+0.2371***
dmc1:+0.3038***
mre110:+0.1336***
mre116:+0.1802***
Grouped
N = 261651 codons
R2 = 0.194***
P(GL)***,P(Expr)** P(dmc1,
mre110)***
-0.2153*** +0.1304*** Co:+0.3181***
nCo:+0.2274***
spo11:+0.3667***
dmc1:+0.4767***
mre110:+0.2293***
mre116:+0.2769***
F GC non-opt: Frequency of GC-ending non-optimal codons, n = 1276 genes
Ala
N = 30071 codons
-0.0855** +0.1573*** Co:+0.1592***
nCo:+0.1124***
spo11:+0.2234***
dmc1:+0.2520***
mre110:+0.1173***
mre116:+0.1586***
Arg
N = 15296 codons
-0.0152NS +0.2595*** Co:+0.0435NS
nCo:+0.0651*
spo11:+0.1235***
dmc1:+0.1255***
mre110:+0.0714*
mre116:+0.0893**
Gly
N = 23663 codons
-0.0689* +0.1643*** Co:+0.1707***
nCo:+0.1559***
spo11:+0.2027***
dmc1:+0.2850***
mre110:+0.1697***
mre116:+0.1397***
Leu
N = 62345 codons
-0.1961*** -0.0819** Co:+0.2238***
nCo:+0.1806***
spo11:+0.2578***
dmc1:+0.3524***
mre110:+0.1106***
mre116:+0.1979***
Pro
N = 23167 codons
-0.1141*** -0.1121*** Co:+0.1576***
nCo:+0.1333***
spo11:+0.1384***
dmc1:+0.2066***
mre110:+0.0792**
mre116:+0.1310***
Thr
N = 22921 codons
-0.0736** -0.0469NS Co:+0.1404***
nCo:+0.1070***
spo11:+0.1571***
dmc1:+0.1914***
mre110:+0.0906**
mre116:+0.0981***
Ser
N = 45898 codons
-0.1153*** -0.0056NS Co:+0.1943***
nCo:+0.1194***
spo11:+0.2200***
dmc1:+0.2990***
mre110:+0.1669***
mre116:+0.1775***
Val
N = 20558 codons
-0.0599* +0.1127*** Co:+0.2433***
nCo:+0.1623***
spo11:+0.1956***
dmc1:+0.2672***
mre110:+0.1468***
mre116:+0.1747***
Grouped
N = 341847 codons
R2 = 0.727***
P(GL)***,P(Expr)***
P(dmc1)***,
P(mre110)NS
-0.2858*** +0.0820** Co:+0.3194***
nCo:+0.2443***
spo11:+0.3526***
dmc1:+ 0.5357***
mre110:+ 0.2620***
mre116:+0.2978***
  1. Spearman Rank Correlations between the frequency of GC-ending optimal or non-optimal codons with gene length, expression, and various recombination measures. For each amino acid, only genes were used for which at least 4 optimal or 4 non-optimal codons were present respectively. Presented for grouped variables are also MR results of variables whose log-transformation did not grossly deviate from a normal distribution. *P < 0.05, **P < 0.01,***P < 0.001, NS = not significant.