The mitochondrial genome ofAcrobeloides varius(Cephalobomorpha) confirms non-monophyly of Tylenchina (Nematoda)

Abstract

The infraorder Cephalobomorpha is a diverse and ecologically important nematode group found in almost all terrestrial environments. In a recent nematode classification system based on SSU rDNA, Cephalobomorpha was classified within the suborder Tylenchina with Panagrolaimomorpha, Tylenchomorpha and Drilonematomorpha. However, phylogenetic relationships among species within Tylenchina are not always consistent, and the phylogenetic position of Cephalobomorpha is still uncertain. In this study, in order to examine phylogenetic relationships of Cephalobomorpha with other nematode groups, we determined the complete mitochondrial genome sequence of Acrobeloides varius, the first sequenced representative of Cephalobomorpha, and used this sequence for phylogenetic analyses along with 101 other nematode species. Phylogenetic analyses using amino acid and nucleotide sequence data of 12 protein-coding genes strongly support a sister relationship between the two cephalobomorpha species A. varius and Acrobeles complexus (represented by a partial mt genome sequence). In this mitochondrial genome phylogeny, Cephalobomorpha was sister to all chromadorean species (excluding Plectus acuminatus of Plectida) and separated from Panagrolaimomorpha and Tylenchomorpha, rendering Tylenchina non-monophyletic. Mitochondrial gene order among Tylenchina species is not conserved, and gene clusters shared between A. varius and A. complexus are very limited. Results from phylogenetic analysis and gene order comparison confirms Tylenchina is not monophyletic. To better understand phylogenetic relationships among Tylenchina members, additional mitochondrial genome information is needed from underrepresented taxa representing Panagrolaimomorpha and Cephalobomorpha.

The Mitochondrial Genome in Nematode Phylogenetics

“…Phylogenetic assessment of this suborder using SSU rDNA recognized Tylenchina as monophyletic, with four infraorders: Tylenchomorpha, Panagrolaimomorpha, Cephalobomorpha, and Drilonematomorpha (De Ley and Blaxter, 2002Blaxter, , 2004. In contrast however, mitogenome trees consistently depict Tylenchina as non-monophyletic (Kim et al, 2015(Kim et al, , 2017(Kim et al, , 2020. In mitochondrial analyses, Aphelenchoidea (one of the Tylenchomorpha superfamilies) and Panagrolaimomorpha are situated separately from Tylenchoidea (Tylenchomorpha) and Cephalobomorpha ( Figure 1B).…”

“…Clade III was again widely accepted as monophyletic (and called Group 8) in a subsequent phylum-wide SSU rDNA analysis that included many more species (Holterman et al, 2006;van Megen et al, 2009). However, recent mitogenome phylogenies strongly support non-monophyly of clade III (suborder Spirurina) (Kang et al, 2009;Park et al, 2011;Kim et al, 2014Kim et al, , 2017Kim et al, , 2020. Specifically, in mtDNA trees, the members of clade III are split into two separate groups: Rhigonematomorpha is nested within Ascaridomorpha, forming a sister clade to Rhabditomorpha and Diplogasteromorpha, while the remaining clade III members, Oxyuridomorpha and Spiruromorpha, form a separate group (Kim et al, 2017(Kim et al, , 2020; Figure 1B).…”

“…However, recent mitogenome phylogenies strongly support non-monophyly of clade III (suborder Spirurina) (Kang et al, 2009;Park et al, 2011;Kim et al, 2014Kim et al, , 2017Kim et al, , 2020. Specifically, in mtDNA trees, the members of clade III are split into two separate groups: Rhigonematomorpha is nested within Ascaridomorpha, forming a sister clade to Rhabditomorpha and Diplogasteromorpha, while the remaining clade III members, Oxyuridomorpha and Spiruromorpha, form a separate group (Kim et al, 2017(Kim et al, , 2020; Figure 1B). Relationships among oxyuridomorphs, spiruromorphs and dracunculoids have varied depending on the type of mitogenome datasets used (nucleotide versus amino acid sequence datasets) and/or the analytic methods applied (Bayesian versus maximum likelihood).…”

“…In a recent nuclear gene tree, Aphelenchoidea members were split: Aphelenchoididae, Parasitaphelenchidae, and Seinuridae were nested within Panagrolaimomorpha (not including Steinernematidae) and were separated from Aphelenchidae, which was sister to the remaining members of Tylenchomorpha (van Megen et al, 2009). In contrast, mitogenome trees have consistently depicted Aphelenchoidea as being monophyletic, positioned away from other plant-parasitic Tylenchoidea members (Tylenchomorpha) and located inside a novel clade containing species from some non-Tylenchomorpha infraorders: Rhabditomorpha, Panagrolaimomorpha, Diplogasteromorpha, Rhigonamtomorpha, Gnathostomatomorpha, and Ascaridomorpha (Kim et al, 2015(Kim et al, , 2017(Kim et al, , 2020. Thus, mitochondrial phylogenies strongly support Tylenchomorpha as non-monophyletic.…”

“…Gene order is so variable in the Enoplea nematodes that even closely related congeneric species may have extremely different gene orders (Tang and Hyman, 2007;Hyman et al, 2011), rendering mitochondrial gene order useless as a phylogenetic character among the thus-far sequenced members of this group. On the other extreme, some members of Rhabditomorpha, Ascaridomorpha, Diplogasteromorpha, Panagrolaimomorpha, and Aphelenchoidea (Tylenchomorpha) are so nearly identical in gene order (Kim et al, 2016(Kim et al, , 2020 that inferring their relationships based on gene order is likewise impossible. The difference in gene arrangement between Chromadorea and its basal group Enoplea also makes rooting the tree problematic when inferring chromadorean geneorder phylogenies.…”