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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