Chromosome-scale assembly of Kazakh individuals using modern genomics approaches

Aiziya Paizulla, Kuanysh Sarkytbayev, Anel Ordabayeva, Asset Z. Daniyarov, Askhat Molkenov, Diana Samatkyzy, Saule Rakhimova, Ainur R. Akilzhanova, Ulykbek Kairov

2025

Full text Open access: Gold Metadata (CSL-JSON)
DOI 10.11134/btp.3s.2025.8
Data confidence 70 medium
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Abstract

Background: Population-specific reference genomes are crucial for accurate genomic analysis and precision medicine applications. Currently, there is a lack of high-quality chromosome- level reference genomes specifically representing the Kazakh population, which limits the effectiveness of biomedical investigations and genomic studies in this demographic. This project aims to address this gap by creating a comprehensive chromosomal-level assembly of Kazakh individuals' whole genomes using advanced genomic technologies, including next- generation sequencing (NGS, Illumina), third-generation sequencing (TGS, Oxford Nanopore), optical genome mapping, and Hi-C chromosomal conformation capture. Materials and methods: We generated chromosome-scale assemblies of Kazakh individuals by integrating multiple modern genomic technologies. Whole-genome sequencing was performed using both long-read and short-read platforms. The assemblies were polished with short-read data, scaffolded with Bionano optical genome maps, and organized at the chromosomal level using Hi-C chromosomal conformation data. Quality assessment was conducted at each stage, and comparative analyses will be performed against other global reference genomes. Results: The project delivered high-quality, chromosome-level assemblies for individuals of the Kazakh population. These assemblies provide insights into unique genetic features, improve the accuracy of population-specific genomic analyses, and will be deposited in open- access repositories for use in biomedical and bioinformatics research worldwide. Acknowledgement: This study is supported by a grant AP23490594 from the Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan. Keywords: Chromosome-scale assembly; Kazakh genome; long-read sequencing; Bionano optical mapping; Hi-C; de novo assembly; population genomics.