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).