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=Volume 13 - 2022

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=ABSTRACT: 
>Background
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.  
>Results
We conducted haplotype assembling for Equus asinu, 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 re-sequencing data of the donkey population.
>Conclusions
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.