title: Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat.
abstract: Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
authors.affiliation: The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China University of Chinese Academy of Sciences, 100049 Beijing, China Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, China.
authors.forename: Huajing
authors.initials: H
authors.lastname: Teng
authors.affiliation: The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China.
authors.forename: Yaohua
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China Beijing Institute of Genomics, Chinese Academy of Sciences, 100101 Beijing, China.
authors.forename: Chengmin
authors.initials: C
authors.lastname: Shi
authors.affiliation: Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, China.
authors.forename: Fengbiao
authors.initials: F
authors.lastname: Mao
authors.affiliation: Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Hou
authors.affiliation: The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China University of Chinese Academy of Sciences, 100049 Beijing, China.
authors.forename: Hongling
authors.initials: H
authors.lastname: Guo
authors.affiliation: Beijing Institutes of Life Science, Chinese Academy of Sciences, 100101, China.
authors.forename: Zhongsheng
authors.initials: Z
authors.lastname: Sun
authors.affiliation: The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China zhangjx@ioz.ac.cn.
authors.forename: Jianxu
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D000835:Animals, Wild; D001483:Base Sequence; D007446:Chromosome Inversion; D002874:Chromosome Mapping; D018389:Codon, Nonsense; D014644:Genetic Variation; D016678:Genome; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D051381:Rats / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
chemical_list: D018389:Codon, Nonsense
keywords: Rattus tanezumi; genetic landscape; next-generation sequencing; single-nucleotide polymorphisms; structural variations