Kai Li, Eleonora Cappelletti, Carey Dessaix, Julia Ciosek, Emily Robyn, Lauren Johnson, Nahla Hussien AbouEl Ela, Xiomara Arias, David L Adelson, Terje Raudsepp, Francesca M Piras, Melissa L Smith, Elizabeth Hudson, Brandon D Pickett, Sergey Koren, Brian P Walenz, Shelise Y Brooks, Christina Sison, Juyun Crawford, Gerard Bouffard, Adam M Phillippy, Donald Miller, Douglas F Antczak, Jonah Cullen, Sam Stroupe, Brian W Davis, Molly McCue, Sian A Durward-Akhurst, Jessica L Petersen, Elena Giulotto, Ted Kalbfleisch
We present telomere-to-telomere genome assemblies of a Thoroughbred horse and a donkey derived from their mule offspring. Now adopted and annotated by NCBI as reference genomes, these assemblies resolve previously inaccessible regions, including satellite arrays, duplications, and telomeres. Equids are known to exhibit an uncoupling between satellite DNA and centromeric function. The completeness of these assemblies enabled annotation of both satellite-based and satellite-free centromeres, as well as non-centromeric satellite loci, revealing notable centromeric plasticity. They also allowed detailed characterization of the variable binding domains of CENP-A-the epigenetic determinant of centromere identity-and CENP-B, whose association with CENP-A, previously considered typical based on a few model organisms, is absent in equids. Comparative analyses of satellite repeats and centromere positions provide new insights into the accelerated karyotypic reshuffling in equid evolution. These assemblies represent foundational resources for equine genomics and support ongoing initiatives such as the Equine Pangenome Project.