3.4 LDH-A genes in the genome
Two copies of the LDH-A gene were identified, one on chromosome 7 and one on chromosome 17. Their amino acid composition showed small differences in the number of residues of leucine, serine, valine, isoleucine, as well as in the charged amino acids histidine (positive), and aspartic acid (negative; Table S8). In allozyme studies, protein products from the LDH-1 locus move closer to the negative (cathodal) pole while products from the LDH-2 locus move more to the positive (or anodal) pole (Allendorf et al., 1984) indicating that LDH-1 products are more positively charged than those from LDH-2 . The difference in number of aspartic acid and histidine indicate that the protein product from chromosome 7 is slightly more positively charged and thus expected to be more cathodal in electrophoresis than the product from the chromosome 17 locus. No large divergence between the two demes were detected in either of the gene copies; gene-wise F ST forLDH-A from the Pool-seq data was 0.154 and 0.187 for the gene copy on chromosome 7 and chromosome 17, respectively. Furthermore, we found no outlier values for LDH-A in any of theF ST analyses of coding regions. However, the 3’ UTR region of the LDH-A on chromosome 17 showed contrasting allele counts between the two pools, and IGV visualization indicated some genetic variation in this region in Deme I, whereas Deme II was fixed across the whole region (Figure S7, Table S9). In contrast, no divergence of patterns between the demes was observed for LDH-Aon chromosome 7 (Figure S8).
The 3’ UTR region on chromosome 17 was also analyzed using the individual WGS data. In contrast to the results from Pool-seq data the individual sequences did not show any difference between the demes. All four individuals showed lack of variation in the region (Figure S9). We also looked at the 3’ UTR region of chromosome 17 in 11 individuals from other lakes. All of these individuals had been scored for allozyme locusLDH-1 and had all been scored as 100/100. Only one of these individuals (from Lake Saxvattnet) showed a similar IGV profile as those from the two demes in Lakes Bunnersjöarna, whereas all the others did not (Figure S9).