FIGURE 3.

Genome assembly of the Madagascar ground gecko. (a) Hi‐C contact map. The intensities of chromatin contacts quantified in Hi‐C data (red) are indicated in the matrix of different genomic regions. The blue frames indicate the putative chromosomal units. (b) An example of manual curation. The white frames indicate the scaffold units before Hi‐C scaffolding. In a part of the magnified view of the contact map shown in (a), the two input scaffolds indicated by the dashed lines on the left were judged to be derived from a single scaffold on the right. (c, d) Snail plots of the genome assembly before (c) and after (d) Hi‐C scaffolding. These plots were produced using BlobTools2 (Challis et al., 2020). The light‐grey spiral at the center shows the cumulative record count on a log scale, with the white lines indicating successive orders of digits. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold of the assembly, and the ranges in orange and light orange indicate the N50 and N90 lengths, respectively. The blue area in the outer layer shows the distribution of GC, AT, and N percentages in the base composition of each scaffold unit