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Table 1 The organism-wide ΔRSCU values determined using genes with the top 5% expression level (when averaged across all nine tissues) and lowest 5% expression level (**P < 0.001), the predicted tRNA numbers, and codon statuses.

From: Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

Amino acid

Codon

(DNA)

Standard anticodon

ΔRSCU

Pa

No. tRNAs

Optimal and non-optimal status

Wobble

anticodon

(optimal)b

Ala

GCT

AGC

+ 0.871

**

35

Opt-codon↑tRNAs

 

Ala

GCC

GGC

−0.344

**

0

–

 

Ala

GCA

UGC

+ 0.518

**

18

–

 

Ala

GCG

CGC

−1.039

**

22

Nonopt-codon↑tRNAs

 

Arg

CGT

ACG

+ 0.463

**

40

–

 

Arg

CGC

GCG

−1.053

**

0

Nonopt-codon↓tRNAs

 

Arg

CGA

UCG

+ 0.185

**

39

–

 

Arg

CGG

CCG

−0.548

**

2

–

 

Arg

AGA

UCU

+ 0.881

**

18

Opt-codon↑tRNAs

 

Arg

AGG

CCU

+ 0.047

 

26

–

 

Asn

AAT

AUU

+ 0.416

**

0

Opt-codonwobble

GUU

Asn

AAC

GUU

−0.244

**

37

Nonopt-codon↑tRNAs

 

Asp

GAT

AUC

+ 0.520

**

0

Opt-codonwobble

GUC

Asp

GAC

GUC

−0.482

**

31

Nonopt-codon↑tRNAs

 

Cys

TGT

ACA

+ 0.368

**

0

Opt-codonwobble

GCA

Cys

TGC

GCA

−0.365

**

38

Nonopt-codon↑tRNAs

 

Gln

CAA

UUG

+ 0.254

**

39

Opt-codon↑tRNAs

 

Gln

CAG

CUG

−0.218

**

37

Nonopt-codon↑tRNAs

 

Glu

GAA

UUC

+ 0.496

**

31

Opt-codon↑tRNAs

 

Glu

GAG

CUC

−0.480

**

18

Nonopt-codon↑tRNAs

 

Gly

GGT

ACC

+ 0.610

**

0

Opt-codonwobble

GCC

Gly

GGC

GCC

−0.709

**

41

Nonopt-codon↑tRNAs

 

Gly

GGA

UCC

+ 0.483

**

19

–

 

Gly

GGG

CCC

−0.383

**

11

–

 

His

CAT

AUG

+ 0.511

**

0

Opt-codonwobble

GUG

His

CAC

GUG

−0.452

**

37

Nonopt-codon↑tRNAs

 

Ile

ATT

AAU

+ 0.603

**

22

Opt-codon↑tRNAs

 

Ile

ATC

GAU

−0.452

**

0

Nonopt-codon↓tRNAs

 

Ile

ATA

UAU

+ 0.045

 

19

–

 

Leu

TTA

UAA

+ 0.537

**

28

Opt-codon↑tRNAs

 

Leu

TTG

CAA

+ 0.383

**

16

–

 

Leu

CTT

AAG

+ 0.409

**

39

–

 

Leu

CTC

GAG

−0.629

**

0

–

 

Leu

CTA

UAG

+ 0.007

 

28

–

 

Leu

CTG

CAG

−0.692

**

30

Nonopt-codon↑tRNAs

 

Lys

AAA

UUU

+ 0.263

**

20

Opt-codon↑tRNAs

 

Lys

AAG

CUU

−0.160

**

50

Nonopt-codon↑tRNAs

 

Phe

TTT

AAA

+ 0.407

**

0

Opt-codonwobble

GAA

Phe

TTC

GAA

−0.265

**

48

Nonopt-codon↑tRNAs

 

Pro

CCT

AGG

+ 0.749

**

36

Opt-codon↑tRNAs

 

Pro

CCC

GGG

−0.359

**

0

–

 

Pro

CCA

UGG

+ 0.483

**

31

–

 

Pro

CCG

CGG

−0.843

**

36

Nonopt-codon↑tRNAs

 

Ser

TCT

AGA

+ 0.731

**

36

Opt-codon↑tRNAs

 

Ser

TCC

GGA

−0.208

**

0

–

 

Ser

TCA

UGA

+ 0.493

**

21

–

 

Ser

TCG

CGA

−0.723

**

15

Nonopt-codon↑tRNAs

 

Ser

AGT

ACU

+ 0.325

**

0

–

 

Ser

AGC

GCU

−0.619

**

60

–

 

Thr

ACT

AGU

+ 0.644

**

35

Opt-codon↑tRNAs

 

Thr

ACC

GGU

−0.223

**

0

–

 

Thr

ACA

UGU

+ 0.493

**

37

–

 

Thr

ACG

CGU

−0.873

**

31

Nonopt-codon↑tRNAs

 

Tyr

TAT

AUA

+ 0.430

**

0

Opt-codonwobble

GUA

Tyr

TAC

GUA

−0.186

**

43

Nonopt-codon↑tRNAs

 

Val

GTT

AAC

+ 0.600

**

26

Opt-codon↑tRNAs

 

Val

GTC

GAC

−0.394

**

0

–

 

Val

GTA

UAC

+ 0.314

**

30

–

 

Val

GTG

CAC

−0.484

**

40

Nonopt-codon↑tRNAs

 

Amino acids with one codon

    

Met

ATG

CAU

  

43

–

 

Trp

TGG

CCA

  

32

–

 

Total tRNAs

    

1391

  
  1. The number of predicted tRNAs are shown [69]. The primary optimal codon per amino acid and its ΔRSCU value are in bold and underlined. The status of an optimal codon that has a relatively high number of tRNAs (≥18) and those with no tRNAs, and thus obligately requiring the use of wobble tRNAs, are shown, as well as the putative wobble anticodon. The status of primary non-optimal codons that have matching tRNA gene numbers substantially in excess of 0 (≥15) and those with few/no tRNAs are indicated. The status categories are further described in the main text. Codons not having primary optimal or non-optimal status are indicated by “--“.a, α = 0.05, all "**" contrasts had P < 0.001, including after Bonferonni correction. b Standard wobble codons provided; see also inosine modified anticodons for codons with no exact matching tRNAs [70, 71].
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BMC Genomics

ISSN: 1471-2164

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