Improvements to prior reference assemblies for chimpanzee and rhesus macaque. (A) Sequencing approach. Top bar: Locations of 26 human X palindromes (blue bands). Gray band shows centromere location. Bottom: Expansion of a single region containing a human X palindrome (solid black box). One or more clones were selected to span orthologous regions in chimpanzee and rhesus macaque (dashed black boxes). Tree shows estimated divergence times from TimeTree (Kumar et al. 2017). (B) Full-length nanopore reads supporting the structure of a single finished chimpanzee clone (CH251-385I8). (C,D) Two primate X palindromes resolved using SHIMS 3.0 that were missing or misassembled in existing X-Chromosome assemblies. (C) Triangular dot plots from the region orthologous to human P9 in chimpanzee assemblies Pan_tro_3.0 (Kuderna et al. 2017), Clint_PTRv2 (Kronenberg et al. 2018), and SHIMS 3.0. (D) Triangular dot plots from the region orthologous to human P8 in rhesus macaque assemblies Mmul_8.0.1 (Zimin et al. 2014), Mmul_10 (Warren et al. 2020), and SHIMS 3.0.
