Flack Nicole, Drown Melissa, Walls Carrie, Pratte Jay, McLain Adam, Faulk Christopher
Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA.
Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA.
NAR Genom Bioinform. 2023 Apr 4;5(2):lqad033. doi: 10.1093/nargab/lqad033. eCollection 2023 Jun.
Pallas's cat, or the manul cat (), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with 's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for . The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for -specific genes. High genome collinearity within permitted alignment-based scaffolding onto the fishing cat () reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
兔狲，又称帕拉斯猫（Otocolobus manul），是一种原产于中亚草原和荒漠草原的小型猫科动物。蒙古和中国的种群聚居地面临着气候变化、栖息地破碎化、偷猎及其他因素带来的日益严峻的挑战。这些威胁，再加上兔狲在动物园的受欢迎程度以及其在进化生物学中的价值，使得改善该物种的基因组资源成为必要。我们使用独立的纳米孔测序技术为兔狲组装了一个2.5Gb、由61个重叠群组成的核基因组组装序列以及一个17097bp的线粒体基因组。主要的核基因组组装序列测序覆盖度为56倍，重叠群N50为118Mb，针对兔狲特异性基因的BUSCO完整性得分达到94.7%。兔狲基因组内的高度共线性使得基于比对的支架构建能够定位到渔猫（Prionailurus viverrinus）参考基因组上。兔狲的重叠群跨越了所有19条猫科染色体，推断的总间隙长度小于400千碱基。经过改进的碱基识别和变异定相产生了一个替代的假单倍型组装序列以及等位基因特异性DNA甲基化调用；在单倍型之间鉴定出61个差异甲基化区域。最近的特征包括经典的印记基因、非编码RNA以及假定的新印记位点。组装好的线粒体基因组成功解决了兔狲核基因组和线粒体DNA系统发育之间现有的不一致性。所有组装草图均由使用七个MinION流动槽产生的158Gb序列生成。
