Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology

被引：21

作者：

Peng, Yongdong ^{[1
]}

Li, Hong ^{[2
]}

Liu, Zhengzhu ^{[1
]}

Zhang, Chuansheng ^{[1
]}

Li, Keqiang ^{[3
]}

Gong, Yuanfang ^{[1
]}

Geng, Liying ^{[4
]}

Su, Jingjing ^{[5
]}

Guan, Xuemin ^{[4
]}

Liu, Lei ^{[6
]}

Zhou, Ruihong ^{[1
]}

Zhao, Ziya ^{[1
]}

Guo, Jianxu ^{[1
]}

Liang, Qiqi ^{[2
]}

Li, Xianglong ^{[1
]}

机构：

[1] Hebei Normal Univ Sci & Technol, Coll Anim Sci & Technol, Hebei Key Lab Specialty Anim Germplasm Resources, Qinhuangdao, Hebei, Peoples R China

[2] Novogene Bioinformat Inst, Beijing 100083, Peoples R China

[3] Hebei Normal Univ Sci & Technol, Coll Math & Informat Sci, Hebei Key Lab Specialty Anim Germplasm Resources, Qinhuangdao, Hebei, Peoples R China

[4] Hebei Normal Univ Sci & Technol, Coll Agron & Biotechnol, Hebei Key Lab Specialty Anim Germplasm Resources, Qinhuangdao, Hebei, Peoples R China

[5] Yanshan Univ, Sch Environm & Chem Engn, Hebei Key Lab Appl Chem, Qinhuangdao, Hebei, Peoples R China

[6] Shandong Agr Univ, Coll Anim Sci & Technol, Tai An, Shandong, Peoples R China

来源：

MOLECULAR ECOLOGY RESOURCES | 2021年 / 21卷 / 06期

基金：

中国国家自然科学基金;

关键词：

chromosome-level genome assembly; conservation; environmental adaptation; evolution; genome annotation; Vulpes lagopus; BETA-CELL GLUCOKINASE; ALOPEX-LAGOPUS; ACYL-COENZYME; SQUALENE MONOOXYGENASE; PHYLOGENETIC ANALYSIS; PYRUVATE-KINASE; BLUE FOXES; RED FOX; GENE; POPULATION;

D O I：

10.1111/1755-0998.13397

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of similar to 7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.

引用

页码：2093 / 2108

页数：16