Table 1

Difference of optimal codons depending on whether they end with -GC or -AT.

Amino acid

Gene length

Expression

Recombination


FOPAT: FOP for aminoacids with AT-ending optimal codons


Ala

N = 53719 codons

+0.0229NS

+0.2546***

Co:-0.0656**

nCo:-0.0217NS

spo11:-0.0856***

dmc1:-0.0540*

mre110:+0.0147NS

mre116:-0.0659**


Arg

N = 43139 codons

+0.0002NS

+0.4301***

Co:+0.0293NS

nCo:+0.0265NS

spo11:+0.0297NS

dmc1:+0.0488NS

mre110:+0.0375NS

mre116:-0.0037NS


Cys

N = 13614 codons

+0.0535*

+0.2293***

Co:-0.0162NS

nCo:-0.0239NS

spo11:-0.0229NS

dmc1:+0.0030NS

mre110:+0.0172NS

mre116:-0.0158NS


Gln

N = 38581 codons

+0.0603*

+0.2076***

Co:-0.0777**

nCo:-0.0546*

spo11:-0.0495NS

dmc1:-0.0873***

mre110:-0.0532NS

mre116:-0.0565*


Glu

N = 65707 codons

+0.1396***

+0.1663***

Co:-0.0658**

nCo:-0.0573*

spo11:-0.0796**

dmc1:-0.1154***

mre110:-0.0252NS

mre116:-0.0822**


Gly

N = 49861 codons

+0.0470NS

+0.4385***

Co:+0.0241S

nCo:+0.0230NS

spo11:+0.0298NS

dmc1:+0.0406NS

mre110:+0.0831**

mre116:-0.0037NS


Pro

N = 43069 codons

+0.0304NS

+0.3114***

Co:-0.0509*

nCo:-0.0292NS

spo11:+0.0105NS

dmc1:-0.0481NS

mre110:+0.0116NS

mre116:-0.0348NS


Grouped

N = 307690 codons

R2 = 0.300***

P(GL)***,P(Expr)***,

P(dmc1)***P(mre110)**

+0.1271***

+0.3732***

Co:-0.0867**

mCo:-0.0556*

spo11:-0.0086***

dmc1:-0.1643***

mre110:-0.0601*

mre116:-0.1074***


FOPGC: FOP for aminoacids with GC-ending optimal codons


Leu

N = 96687 codons

-0.1031***

+0.3690***

Co:+0.1828***

nCo:+0.1451***

spo11:+0.2015***

dmc1:+0.2526***

mre110:+0.1206***

mre116:+0.1344***


Asn

N = 60930 codons

-0.1588***

+0.2880***

Co:+0.2101***

nCo:+0.2000***

spo11:+0.2687***

dmc1:+0.3655***

mre110:+0.1991***

mre116:+0.1866***


Asp

N = 60058 codons

-0.1995***

+0.1485***

Co:+0.1976***

nCo:+0.1500***

spo11:+0.2602***

dmc1:+0.3561***

mre110:+0.1437***

mre116:+0.1997***


Tyr

N = 32887 codons

-0.1850***

+0.2240***

Co:+0.1718***

nCo:+0.1401***

spo11:+0.2499***

dmc1:+0.3186***

mre110:+0.1834***

mre116:+0.1704***


Phe

N = 44129 codons

-0.1103***

+0.2729***

Co:+0.2689***

nCo:+0.1612***

spo11:+0.2628***

dmc1:+0.3413***

mre110:+0.1933***

mre116:+0.1772***


Lys

N = 72564 codons

-0.2207***

+0.3210***

Co:+0.2248***

nCo:+0.1475***

spo11:+0.2843***

dmc1:+0.3632***

mre110:+0.1471***

mre116:+0.2043***


His

N = 21966 codons

-0.1010***

+0.1060***

Co:+0.1193***

nCo:+0.1132***

spo11:+0.1623***

dmc1:+0.2096***

mre110:+0.1086***

mre116:+0.1357***


Grouped

N = 389221 codons R2 = 0.424,

P(GL)***,P(Expr)***

P(dmc1, mre110)***

-0.2604***

+0.4005***

Co:+0.2935***

nCo:+0.2291***

spo11:+0.3667***

dmc1:+0.5090***

mre110:+0.2341***

mre116:+0.2724***


Spearman Rank Correlations between optimal codon use, gene length, expression, and various recombination measures for amino acids and groups of amino acids with either AT- or with GC-ending optimal codons. 1554 genes for which all amino acids were present at least four times were used. 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

Open Data