Whole-genome sequences of DA and F344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer

Guo, Xiaosen, Brenner, Max, Zhang, Xuemei, Laragione, Teresina, Tai, Shuaishuai, Li, Yanhong, Bu, Junjie, Yin, Ye, Shah, Anish A., Kwan, Kevin, Li, Yingrui, Jun, Wang and Gulko, Percio S. (2013) Whole-genome sequences of DA and F344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer. Genetics, 194 4: 1017-1028. doi:10.1534/genetics.113.153049


Author Guo, Xiaosen
Brenner, Max
Zhang, Xuemei
Laragione, Teresina
Tai, Shuaishuai
Li, Yanhong
Bu, Junjie
Yin, Ye
Shah, Anish A.
Kwan, Kevin
Li, Yingrui
Jun, Wang
Gulko, Percio S.
Title Whole-genome sequences of DA and F344 rats with different susceptibilities to arthritis, autoimmunity, inflammation and cancer
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
1943-2631
Publication date 2013-08-01
Year available 2013
Sub-type Article (original research)
DOI 10.1534/genetics.113.153049
Open Access Status Not yet assessed
Volume 194
Issue 4
Start page 1017
End page 1028
Total pages 12
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Language eng
Formatted 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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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