Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China.
Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China.
复制标题
基于二代测序的中国不同毒力弓形虫中国1型株变异检测
DOI：
10.1186/s12864-015-2106-z
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发表时间：
2015-10-30
期刊：
影响因子：
4.4
通讯作者：
Shen J
中科院分区：
文献类型：
--
作者：
Cheng W;Liu F;Li M;Hu X;Chen H;Pappoe F;Luo Q;Wen H;Xing T;Xu Y;Shen J
背景弓形虫是一种细胞内原生动物，影响大多数吸热动物物种，包括人类，感染率很高。弓形虫垂直传播造成流产，对人类构成严重威胁，并导致畜牧业生产遭受巨大损失。与北美和欧洲弓形虫种群结构不同，Chinese 1 (ToxoDB #9) 是中国流行的优势基因型。中国1号分离株中，Wh3和Wh6对小鼠的毒力和致病性不同。然而，人们对它们在基因组水平上的差异知之甚少。因此采用二代测序(NGS)方法来发现表型变异与基因组测序数据的关联以及关键效应子的表达和多态性。结果我们成功对中国1株Wh3和Wh6进行了基因组测序。 Wh3和Wh6的平均测序深度分别为63.91和63.61。通过与 I 型 GT1 菌株的参考基因组进行比较，鉴定了两种分离株的变异。 Wh3和Wh6分别有505,645和505,856个SNP、30,658和30,004个插入缺失、4661和2320个SV以及1942和3080个CNV。在弓形虫特定因子的靶标搜索变异中，发现致密颗粒蛋白3（GRA3）和棒状体颈蛋白3（RON3）分别有35个SNP、2个插入缺失和89个SNP、6个插入缺失。发现 GRA3 和 RON3 在毒力较弱的 Wh6 中的表达水平均高于毒力 Wh3 中的表达水平。中国1型菌株与I型、II型和III型菌株共有多态性GRA15II和ROPI/III。结论对两个菌株进行测序表明，中国1型和I型菌株的基因组结构存在较大的基因组变异。 26 个效应子的测序和 qRT-PCR 分析显示出显着的变异，可能与表型和致病性差异有关。
BackgroundToxoplasma 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.ResultsWe 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.ConclusionsSequencing 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.