In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the two species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in one or two large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation and speciation.

中文翻译：

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家猫 (Felis catus) 和亚洲豹猫 (Prionailurus bengalensis) 的超连续单倍型基因组组装

除了包括最受欢迎的伴侣动物之一外，猫科猫科物种还是遗传和传染病遗传分析以及表型进化和物种形成研究的强大系统。以前基于二倍体的家猫基因组组装已成为猫科动物基因组研究的主要参考。然而，这些版本的复杂和高度重复区域的分辨率很差，有大量未放置的序列是多态性或拷贝数可变的。我们对一只雌性 F1 孟加拉杂交猫的基因组进行了测序，这是一只家猫 (Felis catus) x 亚洲豹猫 (Prionailurus bengalensis) 杂交的后代，使用 PacBio 长序列读取并使用 Illumina 序列读取来自父母的相位 >99。9% 的读入两个物种的单倍型。定相读取的从头组装为家猫和亚洲豹猫产生了高度连续的单倍体基因组组装，两个基因组的重叠群 N50 统计数据均超过 83 Mb。全基因组比对显示 Felis 和 Prionailurus 基因组是共线的，同源 F1 和 E4 染色体之间的细胞遗传学差异代表着丝粒在没有染色体倒位的情况下重新定位的情况。这两个组件都比以前的家猫参考基因组有了显着改进，连续性增加了 100%，并且在一个或两个大型重叠群中捕获了绝大多数染色体臂。我们进一步证明，当三重奏的一个或两个父母不可用时，可以用同一物种的成员实现相对准确的 F1 单倍型定相。这些新的基因组资源将促进猫科动物精准医学、适应和物种形成的研究。