Flack Nicole, Hughes Lauren, Cassens Jacob, Enriquez Maya, Gebeyehu Samrawit, Alshagawi Mohammed, Hatfield Jason, Kauffman Anna, Brown Baylor, Klaeui Caitlin, Mabrouk Islam F, Walls Carrie, Yeater Taylor, Rivas Anne, Faulk Christopher
Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA.
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA.
bioRxiv. 2024 Feb 28:2024.02.20.581252. doi: 10.1101/2024.02.20.581252.
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.
普氏野马（）是一种原产于中亚草原的濒危马科动物。在野外灭绝后，人们开展了多项保护工作来保护该物种，包括圈养繁殖计划、重新引入和监测系统、保护土地以及克隆。拥有高度连续的参考基因组对于支持这些持续的努力至关重要。我们使用牛津纳米孔测序技术，从一匹圈养的普氏野马母马中生成了一个支架水平的2.5Gb核基因组组装和16,002bp的线粒体基因组。所有组装草图均来自单个PromethION R10.4.1流动槽的111Gb序列。线粒体基因组包含标准哺乳动物配置中的37个基因，与家马（）的序列相似度为99.63%。核基因组组装EquPr2包含2,146个支架，N50为85.1Mb，平均深度为43X，BUSCO质量评分为98.92%。EquPr2成功改进了现有的普氏野马参考基因组（Burgud），支架数量减少了25倍，N50增大了至166倍，并具有分阶段的假单倍型。修饰碱基识别显示全球范围内DNA甲基化率为79.5%，羟甲基化率为2.1%。假单倍型之间的等位基因特异性甲基化分析揭示了已知印记基因和以前未报告为印记的位点中有226个差异甲基化区域（DMR）。0.165%的杂合率与该物种之前的估计相符，与其他濒危动物相比具有优势。这个改进后的普氏野马基因组组装将成为保护工作和比较基因组学研究的宝贵资源。
