title: Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China.
abstract: BACKGROUND
  Toxoplasma gondii is an intracellular protozoan that affects most species of endothermic animals including humans with a great infection rate. The vertical transmission of T. gondii causes abortion, constituting a serious threat to humans and leading to great losses in livestock production. Distinct from population structure of T. gondii in North America and Europe, Chinese 1 (ToxoDB #9) is a dominant genotype prevalent in China. Among the isolates of Chinese 1, the Wh3 and Wh6 have different virulence and pathogenicity in mice. However, little has been known about their difference at the genomic level. Thus the next-generation sequencing (NGS) approach was used to discover the association of the phenotypical variations with the genome sequencing data and the expression and polymorphisms of the key effectors.
  
  
  RESULTS
  We successfully sequenced the genome of Chinese 1 strains of Wh3 and Wh6. The average sequencing depths were 63.91 and 63.61 for Wh3 and Wh6, respectively. The variations of both isolates were identified in comparison with reference genome of type I GT1 strain. There were 505,645 and 505,856 SNPs, 30,658 and 30,004 indels, 4661 and 2320 SVs, and 1942 and 3080 CNVs for Wh3 and Wh6, respectively. In target search variations of particular factors of T. gondii, the dense granule protein 3 (GRA3) and rhoptry neck protein 3 (RON3) were found to have 35 SNPs, 2 indels and 89 SNPs, 6 indels, respectively. GRA3 and RON3 were both found to have higher expression levels in less virulent Wh6 than in virulent Wh3. Both strains of type Chinese 1 share polymorphic GRA15II and ROPI/III with type I, II, and III strains.
  
  
  CONCLUSIONS
  Sequencing of the two strains revealed that genome structure of Chinese 1 and type I strains has considerable genomic variations. Sequencing and qRT-PCR analyses of 26 effectors displayed a remarkable variation that may be associated with phenotype and pathogenic differences.
authors.affiliation: Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. cws630@hotmail.com.|Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. cws630@hotmail.com.
authors.forename: Weisheng
authors.initials: W
authors.lastname: Cheng
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. lf0825@live.com.
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. bb41630@163.com.
authors.forename: Man
authors.initials: M
authors.lastname: Li
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. huxiaodonghehe@sina.com.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Hu
authors.affiliation: Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. amuchchenhe@sina.com.|Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. amuchchenhe@sina.com.
authors.forename: He
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. zizalai@yahoo.com.
authors.forename: Faustina
authors.initials: F
authors.lastname: Pappoe
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. luoqingli@ahmu.edu.cn.
authors.forename: Qingli
authors.initials: Q
authors.lastname: Luo
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. huiqinwen@sina.com.|Department of Blood Transfusion, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. huiqinwen@sina.com.
authors.forename: Huiqin
authors.initials: H
authors.lastname: Wen
authors.affiliation: Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. fellowfool@sina.com.
authors.forename: Tian
authors.initials: T
authors.lastname: Xing
authors.affiliation: Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. xyhong1964@163.com.|Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. xyhong1964@163.com.
authors.forename: Yuanhong
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Clinical Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People's Republic of China. shenjilong53@126.com.|Department of Microbiology and Parasitology, Anhui Provincial Laboratory of Pathogen Biology and Anhui Key Laboratory of Zoonoses, Anhui Medical University, Hefei, 230022, People's Republic of China. shenjilong53@126.com.
authors.forename: Jilong
authors.initials: J
authors.lastname: Shen
mesh_terms: D000818:Animals; D002681:China; D019295:Computational Biology / Q000379:methods; D005260:Female; D014644:Genetic Variation; D018503:Genome, Protozoan; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D014122:Toxoplasma / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D014124:Toxoplasmosis, Animal / Q000469:parasitology; D014774:Virulence / Q000235:genetics