NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.
The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia.
BMC Genomics. 2018 Apr 27;19(1):298. doi: 10.1186/s12864-018-4701-2.
Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T. orientalis sourced from Australian herds.
Using de novo assembled sequences and a single nucleotide variant (SNV) analysis pipeline, we found extensive genetic divergence between the T. orientalis genotypes. A genome-wide phylogeny reconstructed to address continued confusion over nomenclature of this species displayed concordance with prior phylogenetic studies based on the major piroplasm surface protein (MPSP) gene. However, average nucleotide identity (ANI) values revealed that the divergence between isolates is comparable to that observed between other theilerias which represent distinct species. Analysis of SNVs revealed putative recombination between the Chitose and Buffeli genotypes and also between Australian and Japanese Ikeda isolates. Finally, to inform future vaccine studies, dN/dS ratios and surface location predictions were analysed. Six predicted surface protein targets were confirmed to be expressed during the piroplasm phase of the parasite by mass spectrometry.
We used whole genome sequencing to demonstrate that the T. orientalis Ikeda, Chitose and Buffeli variants show substantial genetic divergence. Our data indicates that future researchers could potentially consider disease-associated Ikeda and closely related genotypes as a separate species from non-pathogenic Chitose and Buffeli.
东方巴贝斯虫（Apicomplexa：Piroplasmida）多年来一直导致东亚地区的牛临床疾病，其最近在澳大利亚和新西兰牛群中的迅速传播导致因牛死亡、晚期流产和发病率而造成了大量的经济损失。疾病爆发与致病性东方巴贝斯虫基因型 Ikeda 的检测有关，该基因型也负责亚洲的疾病爆发。在这里，我们对源自澳大利亚牛群的一种致病性（Ikeda）和两种非致病性（Chitose、Buffeli）东方巴贝斯虫分离株的基因组草案进行了测序和比较。
使用从头组装的序列和单核苷酸变异（SNV）分析管道，我们发现东方巴贝斯虫基因型之间存在广泛的遗传分化。为解决该物种命名法持续存在的混乱而重建的全基因组系统发育与基于主要血孢子表面蛋白（MPSP）基因的先前系统发育研究一致。然而，平均核苷酸同一性（ANI）值表明，分离株之间的差异与代表不同物种的其他泰勒虫之间观察到的差异相当。SNV 分析显示 Chitose 和 Buffeli 基因型之间以及澳大利亚和日本 Ikeda 分离株之间存在潜在的重组。最后，为了为未来的疫苗研究提供信息，分析了 dN/dS 比值和表面定位预测。通过质谱法证实了六个预测的表面蛋白靶标在寄生虫的血孢子阶段表达。
我们使用全基因组测序证明了东方巴贝斯虫 Ikeda、Chitose 和 Buffeli 变体显示出显著的遗传分化。我们的数据表明，未来的研究人员可能可以将与疾病相关的 Ikeda 及其密切相关的基因型视为与非致病性 Chitose 和 Buffeli 不同的单独物种。
