The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agreeing with previous published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 millions of years ago (Ma), a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated ~305 Ma, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. Additionally, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.

中文翻译：

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对线虫进化和起源的系统发育见解


线虫门代表了地球上最国际化和最丰富的后生动物群之一。在这项研究中，我们重建了线虫门的系统发育树。共对 60 个基因组进行了新测序，属于 8 个线虫目，为 Dorylaimida、Mononchida、Monhysterida、Chromadorida、Triplonchida 和 Enoplida 目提供了第一个低覆盖度基因组。由此产生的系统发育在大多数分支中都得到了很好的解析，拓扑结构在各种重建参数中保持一致。Enoplia 亚类被归为 Nematoda 其余部分的姊妹组，与以前发表的系统发育一致。虽然 Triplonchida 目是单系的，但它没有得到很好的支持，而 Enoplida 目是并系的。具有口管的类群形成单系群;然而，超科 Aphelenchoidea 并不构成单系分支。旋毛虫属和鞭毛虫属被推断在大约 202 百万年前 （马） 共享一个共同的祖先，这比以前认为的要晚得多。所有带有 stomatostylet 的线虫都被认为起源于 ~305 马，对应于从泥盆纪到二叠纪的过渡。Thornia 属被置于 Dorylaimina 和 Nygolaimina 之外，与它在先前研究中的位置不一致。此外，我们测试了全基因组扩增方法，并证明它是获得足够 DNA 用于微观真核生物系统发育研究的一种很有前途的策略。这项研究显着扩展了当前的线虫基因组数据集，并且解析良好的系统发育增强了我们对线虫进化的理解。