Phylogenomic Insights into the Evolution and Origin of Nematoda

Abstract

AbstractThe phylum Nematoda represents one of the most cosmopolitan and abundant metazoans on Earth. In this study, we reconstructed the first phylogenomic tree for phylum Nematoda. A total of 54 genomes belongs to eight nematode orders were newly sequenced, providing the first representatives for orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The obtained phylogeny is well-resolved in most of clades, and topologies are similar across reconstruction parameters. Few conflicts were found within Rhabditida when using different metrics or between amino acid and nucleotides. The subclass Enoplia is placed as sister to the rest of Nematoda, thus supporting the hypothesis of a likely marine origin for the nematode ancestor. The Triplonchida is monophyletic but not well-supported, and Enoplida is paraphyletic. The taxa equipped with the stomatostylet form a monophyletic group, but the superfamily Aphelenchoidea does not form a monophyletic clade. GeneraTrichinellaandTrichurisshared a common ancestor ∼170 mya, considerably later period compared to previous studies. All stomatostylet-bearing nematodes is suggested to have existed ∼250 mya, coinciding with the transition from the Permian to the Triassic period. The genusThorniais placed outside of Dorylaimina and Nygolaimina, disagrees with all previous studies. Additionally, we tested the performance of whole genome amplification, and demonstrated it is a promising strategy in phylogenomic of microscopy eukaryotes. The presented study considerably expanded current nematode genome dataset and well-resolved phylogeny improved our understanding for the origin and evolution of Nematoda.