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.

Stoletzki BMC Evolutionary Biology 2011 11:93   doi:10.1186/1471-2148-11-93

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