Ponomareva Ekaterina, Badiss Ahmed, Sultana Tahera, Yu Qing, Nguyen Hai D T
Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, K1A 0C6 Canada.
Agriculture and Agri-Food Canada, Vineland Station, Ottawa, ON, L0R 2E0 Canada.
J Nematol. 2023 Feb 1;54(1):20220058. doi: 10.2478/jofnem-2022-0058. eCollection 2022 Feb.
The stem and bulb nematode is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas , only known to infect a weed plant (), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of and . We sequenced the genomes of two mixed-stage nematode populations of and two mixed-stage nematode populations of . The assembled genomes of were 228.2 Mb and 239.5 Mb, and the genomes of were 177.0 Mb and 196.3 Mb. Depending on the species, 21,403-27,365 gene models were predicted. Using orthologous group analysis, single-copy and species-specific genes were identified. Primers and probes were designed targeting two species-specific genes in each species. The assays detected as low as 12 pg of DNA from the target species, or as few as five nematodes, with a C of 31 cycles or less. Our study provides genome data for two additional isolates and two isolates, and four new and validated molecular assays to be used for rapid detection and identification of the two species.
茎和球茎线虫是许多作物上的一种毁灭性线虫害虫，在许多国家被列为国际检疫对象，而仅已知感染一种杂草植物（），是一种未受管制且无已知经济重要性的线虫物种。在本研究中，我们利用比较基因组学来鉴定多个基因区域，并开发了用于检测和的新型实时荧光定量PCR检测方法。我们对两个混合发育阶段的线虫种群和两个混合发育阶段的线虫种群进行了基因组测序。组装后的基因组大小分别为228.2 Mb和239.5 Mb，而的基因组大小分别为177.0 Mb和196.3 Mb。根据物种不同，预测出21403 - 27365个基因模型。通过直系同源组分析，鉴定出单拷贝基因和物种特异性基因。针对每个物种的两个物种特异性基因设计了引物和探针。这些检测方法能够检测到低至12 pg的目标物种DNA，或低至五条线虫，循环阈值（C）为31个循环或更低。我们的研究提供了另外两个分离株和两个分离株的基因组数据，以及四种新的且经过验证的分子检测方法，用于快速检测和鉴定这两个物种。
