Table 4 Genes in stratum 1 with markedly different (P<0.1) dN/dS (ω) ratios among the Neurospora tetrasperma mat a and mat A-linked alleles based on the branch model analysis in PAML

From: Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma

Gene

Gene description a

ω mat a b

ω mat A b

Direction of difference

LRT P-value

Concatenated sequences of all stratum 1 genes

0.1321

0.1142

ωmat a>ωmat A

0.3482

Specific genes with differences

 NCU02502

Hypothetical protein similar to S-adenosyl-methionine-sterol-C

>0.0001

0.0001

ωmat a>ωmat A

0.0514

 NCU02510

Clathrin heavy chain

0.0001

0.3233

ωmat A>ωmat a

0.0427

 NCU02633

Hypothetical protein similar to nuclear mRNA splicing factor

>0.0001

0.0001

ωmat a>ωmat A

0.0010

 NCU02675

Hypothetical protein similar to RNA-3′-phosphate cyclase family protein

0.0001

0.13

ωmat A>ωmat a

0.0558

 NCU02761

Hypothetical protein

>0.0001

0.0001

ωmat a>ωmat A

0.0534

 NCU09382

Predicted protein

0.0001

0.6752

ωmat A>ωmat a

0.0496

 NCU09317

Predicted protein

>0.0001

0.0001

ωmat a>ωmat A

0.067

 NCU09310

Conserved hypothetical protein

>0.1311

0.1311

ωmat a>ωmat A

0.0254

 NCU03152

Conserved hypothetical protein

0.3087

0.0001

ωmat a>ωmat A

0.0978

 NCU09142

Hypothetical protein similar to cytoplasmic dynein intermediate chain

0.1328

0.0001

ωmat a>ωmat A

0.0496

 NCU08348

Conserved hypothetical protein

0.0001

0.5494

ωmat A>ωmat a

0.0338

 NCU07362

Hypothetical protein similar to mitochondrial cytochrome b2

0.3567

0.0001

ωmat a>ωmat A

0.0025

 NCU00921

Conserved hypothetical protein

0.4264

>0.4264

ωmat A>ωmat a

0.0936

 NCU00771

Conserved hypothetical protein

0.0001

0.3085

ωmatA>ωmat a

0.0111

 NCU00499

All development altered-1

>0.0001

0.0001

ωmat a>ωmat A

0.0964

 NCU03013

Anchored cell wall protein-10

0.0001

>0.0001

ωmatA>ωmat a

0.0592

  1. Abbreviations: LRT, likelihood ratio test; PAML, phylogenetic analysis by maximum likelihood.
  2. P-values of likelihood ratio tests (LRT) are provided.
  3. aHypothetical proteins are predicted from genomic data, but have no evidence of expression to date; predicted proteins have evidence of expression from ESTs or other mRNA analysis.
  4. bCases with a value beginning with > indicates that the dS level was very low (<0.0001) or equal to zero while dN was markedly >0, wherein PAML assigns no estimate of ω (that is, a default value of 999), but only indicates whether a statistically significant difference is present and the direction of the difference.
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