The root‐knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four “host races” had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4‐gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro‐economic challenges.

中文翻译：

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种群基因组学支持克隆性繁殖以及在最具破坏力的线虫中产生多种独立的寄生能力。

根结线虫是全世界农业中最具破坏力的蠕虫，其中南方根结线虫是分布最广，破坏力最强的物种。鉴于其假定的强制性克隆繁殖，这种寄生和生态学的成功似乎令人惊讶。根据细胞学观察结果怀疑克隆繁殖，但到目前为止，尚未得到种群基因组学数据的证实。作为一个物种，隐孢子虫高度吞噬，具有成千上万种寄主植物。然而，不同的M. incognita分离株表现出宿主相容性的不同和重叠模式。从历史上看，根据兼容植物和不兼容植物的范围定义了四个“宿主种族”。在这项研究中，我们使用种群基因组学来评估（a）该物种的繁殖实际上是否是克隆的；（b）宿主种族遵循潜在的系统发生信号，或者代表多个独立的过渡，以及（c）基因组变异如何与其他重要的生物学特性，例如受影响的农作物和地理分布。我们对覆盖巴西的四个寄主种族的11个隐姓氏梭状芽胞杆菌菌株的基因组进行了测序。通过将这些分离株的基因组读段与隐隐支原体进行比对参考基因组装配，我们确定了点变异。连锁不平衡和4配子测试的分析表明，没有证据的重组，证实的克隆繁殖根结线虫。分离株之间的几个点变化表明与宿主种族，样品的地理起源或收集其的作物没有显着相关性。来自世界其他地方的分离株的添加证实了这种潜在的系统发育信号的缺乏。这表明寄生能力的多方面得失和对不同环境的适应导致了隐孢子虫的广泛宿主范围和广泛的地理分布。从而对其产生了巨大的经济影响。这种无性别的惊人适应性带来了进化和农业经济方面的挑战。