Table 1.
Nucleotide and amino acid sequence diversity and nucleotide sequence divergence in coding regions of recombination genes in a common set of 25 maize inbred lines
| Gene | Alignment length (bp) | Diversity | Divergence | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Nucleotide diversity in the coding region | Amino acid diversity (polymorphic amino acid residues per 100 residues) | d N/d S a | K scale factorb | ||||||
| θ W | π (+/−SE) | π a | π s | π a/π s | |||||
| Dmc1 | 1032 | 0.00436 | 0.00332 +/− 0.000104 | 0.00040 | 0.01269 | 0.032 | 0.87 | 0.013 | 1.74 |
| Mlh1 | 1197 | 0.00310 | 0.00229 +/− 0.000078 | 0.00113 | 0.00600 | 0.188 | 1.66 | 0.157 | 0.43 |
| Mre11A | 2124 | 0.00288 | 0.00229 +/− 0.000048 | 0.00036 | 0.00886 | 0.041 | 0.85 | 0.014 | 1.20 |
| Mre11B | 2019 | 0.00224 | 0.00123 +/− 0.000056 | 0.00112 | 0.00162 | 0.691 | 2.23 | 0.370 | 1.00 |
| Msh4 | 2412 | 0.00231 | 0.00321 +/− 0.000058 | 0.00088 | 0.01054 | 0.083 | 0.62 | 0.074 | 0.82 |
| Mus81-1 | 1089 | 0.00244 | 0.00217 +/− 0.000062 | 0.00182 | 0.00361 | 0.504 | 2.00 | 0.129 | 0.76 |
| Rad51A1 | 873 | 0.00212 | 0.00162 +/− 0.000084 | 0.00000 | 0.00832 | 0.000 | 0.00 | 0.000 | 2.18 |
| Rad51A2 | 666 | 0.00398 | 0.00692 +/− 0.000084 | 0.00406 | 0.01595 | 0.255 | 1.18 | 0.122 | 2.22 |
| Recq4 | 1878 | 0.00268 | 0.00273 +/− 0.000084 | 0.00144 | 0.00724 | 0.199 | 1.45 | 0.231 | 0.42 |
| Spo11-1 | 948 | 0.00168 | 0.00097 +/− 0.000116 | 0.00043 | 0.00265 | 0.162 | 0.52 | 1.172 | 0.73 |
| Spo11-2 | 984 | 0.00458 | 0.00444 +/− 0.000136 | 0.00232 | 0.01085 | 0.214 | 1.31 | 0.244 | -c |
a d N/d S was calculated relative to Z. luxurians, except for Mus81, where it was calculated relative to Z. diploperennis
b The K scale factor describes sequence divergence by measuring the overall size of the phylogenetic tree [107]. Smaller K scale factor values indicate more divergence. We calculated the K scale factors separately for each of the two copies of Mre11 and Rad51 even though maize is the only of the species used in this analysis that has two homologs of these genes. The values differ somewhat for each of the two Mre11 and Rad51 homologs, which could suggest that the two copies are fairly diverged. However, according to genetic studies (see Discussion) the two copies of Rad51 and Mre11 have overlapping functions, which indicates that they can both be treated as functional homologs of the Rad51 and Mre11 genes from other species
c The eukaryote-wide rate of sequence divergence could not be calculated as Spo11-2 forms a separate lineage in plants and is absent from other extant groups of eukaryotes