Chromosome-Level Haplotype Assembly for Equus asinu.

Area of Science:

• Genomics
• Animal Genetics
• Bioinformatics

Background:

• Haplotypes are crucial for understanding individual and population genomes.
• Research on non-model organisms is often limited by the absence of haplotype data.
• Donkeys (Equus asinus) are important non-model organisms with limited genomic haplotype information.

Purpose of the Study:

• To perform haplotype assembly for the Dezhou donkey, a significant non-model organism.
• To establish a chromosome-scale haplotype for an individual Dezhou donkey.
• To create a phased haplotype dataset for a donkey population.

Main Methods:

• Utilized high-depth sequencing data including single-molecule real-time sequencing (×30) and Illumina short-read sequencing (×211).
• Employed high-throughput chromosome conformation capture (×56) for haplotype phasing.
• Applied advanced bioinformatic approaches for haplotype assembly and phasing.

Main Results:

• Achieved a near-complete chromosome-scale haplotype for the Dezhou donkey individual with over 99.7% phase rate.
• Assembled a phased cohort of 156 donkeys.
• Generated a donkey haplotype dataset containing more than 39 million genetic variations.

Conclusions:

• Successfully described the complete chromosome-scale haplotype of the Dezhou donkey.
• Established a valuable genomic resource for donkey research and conservation.
• The developed haplotype dataset will facilitate future studies on donkey population genetics and trait association.