Additional file 2 of The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations
Creators: name: Policarpo, Maxime
name: Legendre, Laurent
name: Germon, Isabelle
name: Lafargeas, Philippe
name: Espinasa, Luis
name: Rétaux, Sylvie
name: Casane, Didier
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig S1. Distribution of pLoF variants. (A) Distribution of each type of pLoF variants in cave populations. (B) Frameshift sizes distribution. Fig S2. Distribution of pLoF alleles in four cave populations.Venn diagram using 9 genomes per population. Numbers correspond to the number of pLoF identified. Genes belonging to the vision, pigmentation or circadian clock datasets and impacted by pLoF mutations are indicated (in red, blue and green respectively). Ensembl gene ID are indicated for genes which are impacted by the same pLoF mutations in the four cave populations. Cave populations where the rgr2 and opn8 deletions were retrieved are also indicated (Δ-rgr2 and Δ-opn8 respectively). Fig S3. Dotterplot between surface and cave genomes. (A) rgr2 and (B) opn8 large deletions. X-axis correspond to the Pachón reference genome assembly (GCA_019721115.1) while Y-axis correspond to the Surface reference genome assembly (GCA_000372685.2). Genomic regions aligned are indicated along the axis. (C) and (D) represent the coverage on these regions (in the surface genome assembly) of one non-deleted individual, one heterozygous individual, and one homozygous deleted individual. Fig S4. Comparison of pLoF variant frequencies obtained in the WGS data and by genotyping with PCR followed by sanger sequencing or by identification in a 3.5% agarose gel. Fig S5. Standard length and eye diameter measures on Toro individuals. Blue lines represent the standard length and red line the eye diameter. Fig S6. pLoF variant genotyping. For each pLoF variant genotyped, the left panel show the corresponding genomic sequence extracted from the surface reference genome (GCA_000372685.2) as well as the primer sequences used (written in blue) and the position of the pLoF variant (highlighted in red). Primer sequences in blue can be retrieved in the Additional file 4. The right panel show examples of homozygous individuals without the pLoF variant (wt/wt), heterozygous individuals (wt/-), and homozygous individuals with the pLoF variant (-/-). Fig S7. Large deletion genotyping. (A) Representation of deleted regions in the cave populations. Exons of genes are represented by blue squares, and exons amplified to genotype these deletions are indicated either with blue lines (exons used as control) or red lines (exons in the deleted regions). The deletion region in cave individuals is represented with dotted lines. (B) The left panel show the expected gel pattern if an individual is not deleted. The right panel show a gel with homozygous deleted individuals (-) and with non-deleted individuals (+) for which we cannot differentiate between heterozygous or homozygous non-deleted. Table S1. Go-term enrichment. (A) GO-term enrichment analysis results with all human orthologous genes. Only significant GO-terms are shown. (B) GO-term enrichment analysis results with all zebrafish orthologous genes, using the “GO Biological Process GeneRIF Predicted Z-score” database. The 25 top results are shown, but neither of those are significant. (C) GO-term enrichment analysis results with all zebrafish orthologous genes, using the “Phenotype GeneRIF Predicted Z-score” database. The 25 top results are shown, but only the 21 first terms are significant.