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

Abstract

Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.

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

“…Compared to enoplean species, the mitochondrial gene order of chromadorean nematodes is relatively conserved, and gene order similarity among certain groups has been interpreted as additional supporting evidence for their phylogenetic affinity, although an idiosyncratic pattern has also been reported in some species (Kim et al, 2014;. Among nematode mt genomes reported thus far, gene arrangement patterns in most members of Rhabditomorpha (70 of 72 species), Ascaridomorpha (24 of 28 species), Diplogasteromorpha (one of two species), Aphelenchoididae (all three species except for trnN ) and Steinernema (2 out of 4 species) are identical except for some idiosyncratic gene arrangements and a few minor translocations of tRNAs in some species (Jex et al, 2010;Kim et al, 2018;Liu et al, 2013;Montiel et al, 2006;Wang et al, 2016).…”

“…Duplication of tRNA genes has been occasionally reported from other nematode mitochondrial genomes such as Camallanus cotti (Zou et al, 2017), Dracunculus medinensis (Genbank accession no. NC_016019, Clark et al, 2016) and Ruizia karukerae (Kim et al, 2018).…”

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia)

“…3) also has a different pattern of arrangement, where we recovered two separate mitochondrial chromosomes. Multipartite mitochondrial genomes have been well documented in metazoans where the size and number of chromosomes vary remarkably (Watanabe et al 1999;Wei et al 2012;Lavrov and Pett 2016;Phillips et al 2016;Kim et al 2018). Despite the attempts to explain how and why a multipartite genome may have arisen, it is still unclear.…”

The Mitochondrial Genome in Nematode Phylogenetics

“…Beyond its phylogenetic utility, the sequencing and study of nematode mitogenomes has the potential to produce other interesting biological insights. In rare instances, some nematode species with multiple circular chromosomes have been sequenced (Armstrong et al, 2000;Hunt et al, 2016;Phillips et al, 2016;Kim et al, 2018). The discovery of multiple mitochondrial chromosomes makes nematodes one of only four known animal phyla with such unusual mitogenome architecture (the other three are dicyema, arthropods, and rotifers; Watanabe et al, 1999;Suga et al, 2008;Shao et al, 2012).…”

“…The discovery of multiple mitochondrial chromosomes makes nematodes one of only four known animal phyla with such unusual mitogenome architecture (the other three are dicyema, arthropods, and rotifers; Watanabe et al, 1999;Suga et al, 2008;Shao et al, 2012). In a recent study describing the existence of two distinct mitochondrial chromosomes in the nematode Ruizia karukerae, small-scale sequence differences (i.e., a single non-synonymous nucleotide substitution) between duplicated copies of cox2 gene on each of the two chromosomes suggest that the process of chromosome multiplication might be at an early stage in this group (Kim et al, 2018). It is interesting to note that nematode species with multipartite mitochondrial chromosomes are so far all parasitic (Globodera ellingtonae, G. pallida, G. rostochiensis [plant parasitic]; Rhabditophanes sp.…”