donkey and horse Genome sequencing and assembly

In this project, we aimed to achieve telomere - to - telomere (T2T) level genome assemblies for both horse and donkey.Blood tissues were carefully collected from representative horse and donkey specimens. For genome assembly, we utilized a comprehensive set of sequencing data. PacBio HiFi data, renowned for its high base - calling accuracy, was used. Additionally, we incorporated Oxford Nanopore Technologies (ONT) data with an N50 greater than 100k and ultra - long ONT data with an N50 greater than 200k. Hi - C data, essential for scaffolding and determining chromosomal structure, was also included.For the horse, our objective was to assemble its 62 autosomes and the XY sex chromosomes. Regarding the donkey, we aimed to assemble its 60 autosomes and the XY sex chromosomes.To enhance the assembly quality further, we used next - generation sequencing (NGS) short - read data to fill gaps in the draft genomes. Moreover, chromatin immunoprecipitation sequencing (ChIP - seq) data was applied to accurately identify centromeric regions, which are crucial elements in chromosomal organization.Through these integrated and systematic methods, we successfully completed the T2T - level genome assemblies for both horse and donkey. These high - quality genomic resources will facilitate in - depth research in equine genetics, evolution, and other related fields.

本研究旨在完成马与驴的端粒到端粒（Telomere-to-Telomere, T2T）级基因组组装。本研究从具有代表性的马和驴标本中精心采集了血液组织。针对基因组组装工作，我们采用了一套完整的测序数据集：使用了以碱基识别精度见长的PacBio HiFi测序数据；此外还纳入了N50大于100k的牛津纳米孔技术（Oxford Nanopore Technologies, ONT）测序数据，以及N50大于200k的超长ONT测序数据；同时纳入了在基因组支架构建与染色体结构解析中发挥关键作用的Hi-C测序数据。针对马的基因组组装，我们的目标是覆盖其62条常染色体与XY性染色体；而就驴而言，我们计划组装其60条常染色体与XY性染色体。为进一步提升组装质量，我们使用了下一代测序（Next-Generation Sequencing, NGS）短读长测序数据来填补草图基因组中的序列缺口。此外，我们还利用染色质免疫共沉淀测序（Chromatin Immunoprecipitation Sequencing, ChIP-seq）数据精准识别着丝粒区域，该区域是染色体结构组织的核心元件。通过上述整合且系统化的研究方法，我们成功完成了马与驴的T2T级基因组组装。这批高质量的基因组资源将为马科动物遗传学、演化生物学及其他相关领域的深入研究提供重要支撑。