CNRS-UPS-IRD, UMR5174, EDB, 118 route de Narbonne, Université Paul Sabatier, 31062 Toulouse, France.
IRD, Cirad, University of Montpellier II, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France.
Genes (Basel). 2019 Feb 25;10(2):175. doi: 10.3390/genes10020175.
is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environments. Previous studies on nuclear ribosomal DNA (nrDNA) suggested a close phylogenetic relationship between and , despite their different modes of reproduction and geographical distribution. In order to clarify the evolutionary history of these two species and explore their molecular intraspecific diversity, we sequenced the genome of 12 isolates, representing populations of worldwide origins, and two South American isolates of . -mer analysis of their nuclear genome and the detection of divergent homologous genomic sequences indicate that both species show a high proportion of heterozygous sites (ca. 1⁻2%), which had never been previously reported in facultative meiotic parthenogenetic RKNs. These analyses also point to a distinct ploidy level in each species, compatible with a diploid and a triploid . Phylogenetic analyses of mitochondrial genomes and three nuclear genomic sequences confirm close relationships between these two species, with being a putative parent of . In addition, comparative mitogenomics of those 12 isolates with a Chinese published isolate reveal only 15 polymorphisms that are phylogenetically non-informative. Eight mitotypes are distinguished, the most common one being shared by distant populations from Asia and America. This low intraspecific diversity, coupled with a lack of phylogeographic signal, suggests a recent worldwide expansion of .
是一种兼性减数分裂孤雌生殖根结线虫（RKN），严重威胁着全球农业。我们对其起源、基因组结构和种内多样性知之甚少。这些信息将更好地了解这种线虫如何在许多不同的环境中成功地损害水稻。先前对核核糖体 DNA（nrDNA）的研究表明，尽管 和 具有不同的繁殖方式和地理分布，但它们在系统发育上具有密切的关系。为了阐明这两个物种的进化历史并探索它们的分子种内多样性，我们对 12 个代表全球起源种群的 分离株和两个南美 分离株进行了基因组测序。-mer 分析其核基因组和检测到的分歧同源基因组序列表明，这两个物种都表现出高比例的杂合位点（约 1-2%），这在以前的兼性减数分裂孤雌生殖 RKN 中从未报道过。这些分析还表明，每个物种都有一个独特的倍性水平，与二倍体 和三倍体 相匹配。线粒体基因组和三个核基因组序列的系统发育分析证实了这两个物种之间的密切关系， 是 的潜在亲本。此外，对这 12 个分离株与中国发表的一个分离株的比较线粒体基因组学研究仅揭示了 15 个在系统发育上无信息的多态性。区分出了 8 种 mitotypes，最常见的一种存在于亚洲和美洲的遥远种群中。这种低的种内多样性，加上缺乏系统地理信号，表明 的全球扩张是最近发生的。
