Figure 4.

Assembly of the SAACsand chromosome Y

A. Bandage visualization of acrocentric chromosomes. The left panel shows that the short arms of the ten acrocentric chromosomes are entangled together, while the long arms of each pair of homologous chromosomes are separately twisted. The right panel shows the enlargement of the entangled short arms. The constitute block of chromosomes is colored according to the haplotype and chromosome it is assigned. B. Sequence similarity among the SAACs. The ten SAACs are permutated along the circumference. Pairwise alignments between heterogenous chromosomes with length > 10 kb and identity > 90% are linked by curves. The orange and blue colors and their depth of the curves indicate the direction and identity of the alignment as displayed in the legend. C. The PCoA plot of the short arms and long arms of the acrocentric chromosomes based on their distance in k-mer composition. D. The structure of the complete chromosome YAO-Y. Peak charts show the GC content, coverage of mapped HiFi and ONT reads (> 100 kb) along YAO-Y. The middle panel shows the positions of the ampliconic genes RBMY, DAZ, and TSPY on YAO-Y. The bottom panel is the alignment dot plot of the tandem repeats on YAO-Y visualized by StainedGlass, with the dot color indicating sequence identity. SAAC, short arms of acrocentric chromosome; PCoA, principal co-ordinates analysis; ONT, Oxford Nanopore Technologies.