title: Whole-genome sequences of DA and F344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer.
abstract: DA (D-blood group of Palm and Agouti, also known as Dark Agouti) and F344 (Fischer) are two inbred rat strains with differences in several phenotypes, including susceptibility to autoimmune disease models and inflammatory responses. While these strains have been extensively studied, little information is available about the DA and F344 genomes, as only the Brown Norway (BN) and spontaneously hypertensive rat strains have been sequenced to date. Here we report the sequencing of the DA and F344 genomes using next-generation Illumina paired-end read technology and the first de novo assembly of a rat genome. DA and F344 were sequenced with an average depth of 32-fold, covered 98.9% of the BN reference genome, and included 97.97% of known rat ESTs. New sequences could be assigned to 59 million positions with previously unknown data in the BN reference genome. Differences between DA, F344, and BN included 19 million positions in novel scaffolds, 4.09 million single nucleotide polymorphisms (SNPs) (including 1.37 million new SNPs), 458,224 short insertions and deletions, and 58,174 structural variants. Genetic differences between DA, F344, and BN, including high-impact SNPs and short insertions and deletions affecting >2500 genes, are likely to account for most of the phenotypic variation between these strains. The new DA and F344 genome sequencing data should facilitate gene discovery efforts in rat models of human disease.
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xiaosen
authors.initials: X
authors.lastname: Guo
authors.forename: Max
authors.initials: M
authors.lastname: Brenner
authors.forename: Xuemei
authors.initials: X
authors.lastname: Zhang
authors.forename: Teresina
authors.initials: T
authors.lastname: Laragione
authors.forename: Shuaishuai
authors.initials: S
authors.lastname: Tai
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Li
authors.forename: Junjie
authors.initials: J
authors.lastname: Bu
authors.forename: Ye
authors.initials: Y
authors.lastname: Yin
authors.forename: Anish A
authors.initials: AA
authors.lastname: Shah
authors.forename: Kevin
authors.initials: K
authors.lastname: Kwan
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Wang
authors.initials: W
authors.lastname: Jun
authors.forename: Pércio S
authors.initials: PS
authors.lastname: Gulko
mesh_terms: D000818:Animals; D001168:Arthritis / Q000235:genetics; D001327:Autoimmune Diseases / Q000235:genetics; D001483:Base Sequence; D020224:Expressed Sequence Tags; D020022:Genetic Predisposition to Disease; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D007249:Inflammation / Q000235:genetics; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009369:Neoplasms / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D011914:Rats, Inbred BN; D011916:Rats, Inbred F344 / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion
keywords: BN; DA; F344; Rattus norvegicus; next-generation whole-genome sequencing (NGS); whole-genome sequencing