The complete mitochondrial genome of Koerneria sudhausi (Diplogasteromorpha: Nematoda) supports monophyly of Diplogasteromorpha within Rhabditomorpha

Abstract

Testing hypotheses of monophyly for different nematode groups in the context of broad representation of nematode diversity is central to understanding the patterns and processes of nematode evolution. Herein sequence information from mitochondrial genomes is used to test the monophyly of diplogasterids, which includes an important nematode model organism. The complete mitochondrial genome sequence of Koerneria sudhausi, a representative of Diplogasteromorpha, was determined and used for phylogenetic analyses along with 60 other nematode species. The mtDNA of K. sudhausi is comprised of 16,005 bp that includes 36 genes (12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) encoded in the same direction. Phylogenetic trees inferred from amino acid and nucleotide sequence data for the 12 protein-coding genes strongly supported the sister relationship of K. sudhausi with Pristionchus pacificus, supporting Diplogasteromorpha. The gene order of K. sudhausi is identical to that most commonly found in members of the Rhabditomorpha + Ascaridomorpha + Diplogasteromorpha clade, with an exception of some tRNA translocations. Both the gene order pattern and sequence-based phylogenetic analyses support a close relationship between the diplogasterid species and Rhabditomorpha. The nesting of the two diplogasteromorph species within Rhabditomorpha is consistent with most molecular phylogenies for the group, but inconsistent with certain morphology-based hypotheses that asserted phylogenetic affinity between diplogasteromorphs and tylenchomorphs. Phylogenetic analysis of mitochondrial genome sequences strongly supports monophyly of the diplogasteromorpha.

Complete Mitogenome of Cruznema tripartitum Confirms Highly Conserved Gene Arrangement within Family Rhabditidae

“…3 ). In general, the phylogeny we revealed was congruent with previously published phylogeny inferred by rRNA genes ( Blaxter et al, 1998 ; De Ley and Blaxter, 2004 ; Holterman et al, 2006 ; Meldal et al, 2007 ) or mitogenome ( Kim et al, 2015 , 2017). The family Rhabditidae is paraphyletic, containing a moderately supported major clade (BS = 87) and a separated Diploscapter coronatus sistering to several genera in Rhabditina, Tylenchina, and Spirurina.…”

“…Although there are over 200 nematode mitogenomes that have been sequenced, most of them are from economically important species or zooparasitic species ( Kern et al, 2020 ), and very rarely are they from the free-living taxa. This bias in selection of taxa is partly a result of sequencing obstacles, as a majority of genomes have been acquired by long PCR together with Sanger sequencing technology (e.g., Hu et al, 2002 ; Kim et al, 2015 , 2017 ). Given that mitogenome is highly variable while a closely related reference genome is often missing, a successful primer design and PCR amplification is practically difficult and time-consuming.…”

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

“…The PCGs were biased towards T-rich codons (more than 2 Ts per triplet), similar to other chromadorean nematodes 16 , 19 , 21 – 23 . The three most commonly used codons from each chromosome were all T-rich: TTT (11.3%), TTA (8.4%) and ATT (6.2%) for chromosome I and TTT (11.3%), TTA (9.9%) and ATT (7.2%) for chromosome II (Supplementary Table S1 ).…”

The Mitochondrial Genome in Nematode Phylogenetics

“…Finally, another contribution of mitochondrial phylogenetics is strong support for the novel clade mentioned above (Rhabditomorpha, Panagrolaimomorpha, Diplogasteromorpha, Rhigonematomorpha, Gnathostomatomorpha, and Ascaridomorpha) with Aphelenchoidea placed within this group. In this clade, the position of Diplogasteromorpha is nested within Rhabditomorpha, and Rhigonematomorpha is sister to the heterakoid species (Ascaridomorpha) (Kim et al, 2014(Kim et al, , 2016(Kim et al, , 2017. The close relationship between rhigonematomorphs and ascaridomorphs is consistent with SSU rDNA trees, but those trees only produced very weak support for this ascaridomorph-rhigonematomorph association (Smythe et al, 2006;Nadler et al, 2007;van Megen et al, 2009).…”

“…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.…”