De Novo Genome Assemblies of Kazakh Horses: Adai, Zhabe, Mugalzhar and Naiman

Kazakh horses represent an important cultural heritage of the Kazakh people, shaped over thousands of years across the territory of present-day Kazakhstan. Long-term adaptation to extreme natural conditions has led to the development of a unique set of characteristics that ensure the high survivability, ecological plasticity and economic value of these horses. Long- and short-read sequencing was performed for three breeds (Adai, Zhabe, Mugalzhar), while Naiman was sequenced exclusively with nanopore long-read data. The resulting reads were assembled, and the genomes were subsequently annotated. The assembled genomes showed high contiguity with an average contig N50 value of 9.68 Mb (9,681,711 bp) for Adai, Zhabe and Mugalzhar, while the resulting contig N50 was 17.09 Mb (17,090,216 bp) for Naiman, and average assembly length was 2.42 Gb (2,442,471,376 bp). These are individual reference assemblies that establish foundations for future comparative genomics and pangenome development. Gene annotation yielded 19,584, 19,941, 18,695 and 20,572 protein-coding genes for Adai, Zhabe, Mugalzhar and Naiman, respectively. These assemblies complement existing assemblies for future genetic analysis, research into the geographic and breed origins of domestic horses, and breed conservation efforts, and will contribute to ongoing equine pangenome efforts.