Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis).
Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis).
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DOI：
10.1093/jhered/esaa057
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发表时间：
2021-03-29
期刊：
影响因子：
--
通讯作者：
Murphy WJ
中科院分区：
文献类型：
--
作者：
Bredemeyer KR;Harris AJ;Li G;Zhao L;Foley NM;Roelke-Parker M;O'Brien SJ;Lyons LA;Warren WC;Murphy WJ
除了最受欢迎的伴侣动物之一之外，猫科动物还可以作为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。先前基于二倍体的家猫基因组组装已成为猫科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较差，存在大量多态性或拷贝数可变的未定位序列。我们对雌性 F1 孟加拉杂交猫的基因组进行了测序，该猫是家猫 (Felis catus) 与亚洲豹猫 (Prionailurus bengalensis) 杂交的后代，使用 PacBio 长序列读数并使用来自父母的 Illumina 序列读数将 > 99.9% 的读数定相到两个物种的单倍型中。分阶段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 统计数据都超过 83 Mb。全基因组比对显示，猫科动物和原毛虫基因组是共线的，同源 F1 和 E4 染色体之间的细胞遗传学差异代表了在没有染色体倒位的情况下着丝粒重新定位的情况。与之前的家猫参考基因组相比，这两个组件均具有显着改进，连续性提高了 100%，并捕获了 1 或 2 个大型重叠群中的绝大多数染色体臂。我们进一步证明，当三人组的一个或两个亲本都不可用时，同一物种的成员可以实现相对准确的 F1 单倍型定相。这些新颖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。
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 2 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 1 or 2 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.
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影响因子：
30.8
作者：
Lyons, LA;Laughlin, TF;OBrien, SJ
通讯作者：
OBrien, SJ
影响因子：
3
作者：
Korneliussen TS;Albrechtsen A;Nielsen R
通讯作者：
Nielsen R
在高度濒临灭绝的伊比利亚山脉中，经常性人口瓶颈后的极端基因组侵蚀。
影响因子：
12.3
作者：
Abascal F;Corvelo A;Cruz F;Villanueva-Cañas JL;Vlasova A;Marcet-Houben M;Martínez-Cruz B;Cheng JY;Prieto P;Quesada V;Quilez J;Li G;García F;Rubio-Camarillo M;Frias L;Ribeca P;Capella-Gutiérrez S;Rodríguez JM;Câmara F;Lowy E;Cozzuto L;Erb I;Tress ML;Rodriguez-Ales JL;Ruiz-Orera J;Reverter F;Casas-Marce M;Soriano L;Arango JR;Derdak S;Galán B;Blanc J;Gut M;Lorente-Galdos B;Andrés-Nieto M;López-Otín C;Valencia A;Gut I;García JL;Guigó R;Murphy WJ;Ruiz-Herrera A;Marques-Bonet T;Roma G;Notredame C;Mailund T;Albà MM;Gabaldón T;Alioto T;Godoy JA
通讯作者：
Godoy JA
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL
影响因子：
4.4
作者：
Ghurye J;Pop M;Koren S;Bickhart D;Chin CS
通讯作者：
Chin CS