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.
Highlights
The majority of metazoan mitochondrial genomes have a well-conserved structure and consist of a single circular chromosome, ranging from 14 to 20 kb and containing 37 genes: 13 protein-coding genes (PCGs), two ribosomal RNA genes and 22 transfer RNA genes[1,2]
To locate the remaining genes not found on our assembly of chromosome I, we determined the sequences of partial fragments of cob, nad[1] and nad[4] individually and designed three species-specific primer sets (RP9/RP10, RP11/RP12 and RP13/RP14) (Table 2) for long polymerase chain reaction (PCR)
These were used to amplify and sequence three overlapping fragments [nad1-cob (2.8 kb), cob-nad[4] (2.3 kb) and nad4-nad[1] (2.5 kb)], which formed a second circular mtDNA molecule, which consisted of 7,647 nucleotides and contained seven PCGs and 16 transfer RNA (tRNA) genes (Fig. 1, Table 1)
Summary
The majority of metazoan mitochondrial genomes have a well-conserved structure and consist of a single circular chromosome, ranging from 14 to 20 kb and containing 37 genes: 13 protein-coding genes (PCGs) (atp[6], atp[8], cob, cox[1,2,3], nad[1,2,3,4,5,6] and nad4l), two ribosomal RNA (rRNA) genes (rrnL and rrnS) and 22 transfer RNA (tRNA) genes[1,2]. Mitochondrial genomes are fairly conserved in structure and gene content, they differ from other metazoans in some features. In four nematode species the mitochondrial genome has been found to be divided into multiple chromosomes[10,11,12,13] The reasons underlying these structural abnormalities are unclear, and the sequencing of additional mitogenomes is needed in order to better understand common features of this unusual phenomenon. In this study we report the complete mitochondrial genome sequence of Ruizia karukerae, a member of the infraorder Rhigonematomorpha, a group of about 150 named nematode species that have a direct parasitic life cycle and use millipedes as their final host[20]. The mitochondrial genome of R. karukerae is made up of two circular chromosomes of similar size, each encoding mostly different genes
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