Table 2.
Effect of base composition independent of translational selection.
| 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*** |
| FGCnon-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*** |
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.