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Table 1 Comparison of transition and transversion mutations among 513 total changes at 378 nucleotide positions among the aligned histone H3 sequences in the genome of Pseudocercospora fijiensis

From: Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene

Site categorya

Mutation typeb

Count (percent)c

deRIP consensus

RIP consensus

Conserved

—d

186

180

Non-degenerate

 

234

233

 Conserved

–

142 (60.7)

135 (57.9)

 Tv

Non-Synonymous

56 (23.9)

55 (23.6)

 Ti from gH3 → rH3

Non-Synonymous

23 (9.8)

32 (13.7)

 Ti from rH3 → gH3

Non-Synonymous

13 (5.6)

11 (4.7)

Two-fold degeneratee

 

36

37

 Conserved

–

20 (55.6)

20 (54.1)

 Tv

Non-Synonymous

0 (0)

1 (2.7)

 Ti from gH3 → rH3

Synonymous

15 (41.7)

15 (40.5)

 Ti from rH3 → gH3

Synonymous

1 (2.8)

1 (2.7)

Four-fold degenerate

 

51

51

 Conserved

–

8 (15.7)

9 (17.6)

 Tv

Synonymous

21 (41.2)

20 (39.2)

 Ti from gH3 → rH3

Synonymous

16 (31.4)

16 (31.4)

 Ti from rH3 → gH3

Synonymous

6 (11.8)

6 (11.8)

Variable

 

192

198

 Tv

–

100 (52.1)

99 (50)

 Ti from gH3 → rH3

–

70 (36.5)

80 (40.4)

 Ti from rH3 → gH3

–

22 (11.5)

19 (9.6)

  1. aNon-degenerate sites are those at which any change in nucleotide results in an amino acid substitution; Two-fold degenerate sites are those at which only two of the four possible nucleotides specify the same amino acid; Four-fold degenerate sites are those at which all four nucleotides specify the same amino acid; Variable sites are those where the degeneracy status varies among the sequences being compared; Tv Transversion mutations, Ti Transition mutations, gH3 Original histone H3 sequence, rH3 H3-like sequences in transposable elements; The direction of change, either from gene (g) to repeat (r) or from repeat to gene is indicated by an arrow
  2. bSynonymous mutations cause no change in amino acid; Non-synonymous mutations lead to an amino acid substitution
  3. cCompared to a consensus sequence derived with repeat-induced point mutations present (RIP consensus) or after they were removed (deRIP consensus)
  4. dNot applicable
  5. eIncludes the only three-fold degenerate change in an isoleucine codon