The genome of Przewalski’s horse ( Equus ferus przewalskii ).
Abstract: The Przewalski's horse ( ) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse ( ). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
Publication Date: 2024-02-28 PubMed ID: 38464182PubMed Central: PMC10925127DOI: 10.1101/2024.02.20.581252Google Scholar: Lookup
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Summary
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This research records the creation of an advanced reference genome for the Przewalski’s horse, an endangered horse breed. The genome was created using Oxford Nanopore sequencing and will facilitate further conservation efforts and comparative genetic studies.
Overview of Methodology
- The researchers used Oxford Nanopore sequencing technology to develop a highly contiguous reference genome for the Przewalski’s horse.
- The sequencing for the genome was done from a single PromethION R10.4.1 flow cell using 111 Gb of sequence data from a captive Przewalski’s mare.
- The constructed genome has 2,146 scaffolds with an N50 statistic (benchmark measurement of assembly quality) of 85.1 Mb, a mean depth of 43X, and a BUSCO quality score of 98.92%.
The Mitogenome
- The mitogenome is made up of 16,002 base pairs (bp) and contains 37 standard mammalian genes.
- The similarity between the Przewalski’s horse mitogenome and that of the domestic horse is 99.63%, indicating a strong genetic correlation between the two.
The Nuclear Assembly
- The construction of the nuclear assembly, named EquPr2, marks a significant improvement on the previous Przewalski’s horse reference genome (Burgud).
- Compared to Burgud, EquPr2 has 25-fold fewer scaffolds and a 166-fold larger N50, indicating a more complete and accurate genomic representation.
- The assembly also contains phased pseudohaplotypes, which are representative sets of chromosome pairs for the species.
Methylation and Differential Methylation
- Methylation at 79.5% and hydroxymethylation at 2.1% were revealed by modified basecalls. This refers to changes in the DNA sequence which can alter the genetic information.
- Between pseudohaplotypes, there were 226 differentially methylated regions (DMRs) identified. These included regions of known imprinted genes and loci previously unreported as imprinted.
Benefits of New Assembly
- The heterozygosity rate of 0.165% matches previous estimates for the species, showing consistency with preexisting genetic data.
- The advanced Przewalski’s horse assembly provides a valuable tool for future conservation efforts.
- Furthermore, this comprehensive genome can serve in comparative genomics studies, facilitating our understanding of horses and mammals in general.
Cite This Article
APA
Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C.
(2024).
The genome of Przewalski’s horse ( Equus ferus przewalskii ).
bioRxiv, 2024.02.20.581252.
https://doi.org/10.1101/2024.02.20.581252 Publication
Researcher Affiliations
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