AUTHOR=Miao Xinyao , Yu Yonghan , Zhao Zicheng , Wang Yinan , Qian Xiaobo , Wang Yonghui , Li Shengbin , Wang Changfa 

TITLE=Chromosome-Level Haplotype Assembly for Equus asinu

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.738105

DOI=10.3389/fgene.2022.738105

ISSN=1664-8021

ABSTRACT=<p><bold>Background:</bold> Haplotype provides significant insights into understanding genomes at both individual and population levels. However, research on many non-model organisms is still based on independent genetic variations due to the lack of haplotype.</p><p><bold>Results:</bold> We conducted haplotype assembling for <italic>Equus asinu</italic>, a non-model organism that plays a vital role in human civilization. We described the hybrid single individual assembled haplotype of the Dezhou donkey based on the high-depth sequencing data from single-molecule real-time sequencing (×30), Illumina short-read sequencing (×211), and high-throughput chromosome conformation capture (×56). We assembled a near-complete haplotype for the high-depth sequenced Dezhou donkey individual and a phased cohort for the resequencing data of the donkey population.</p><p><bold>Conclusion:</bold> Here, we described the complete chromosome-scale haplotype of the Dezhou donkey with more than a 99.7% phase rate. We further phased a cohort of 156 donkeys to form a donkey haplotype dataset with more than 39 million genetic variations.</p>