Comparative mitochondrial genomics reveals a possible role of a recent duplication of NADH dehydrogenase subunit 5 in gene regulation

Abstract

Mitochondrial genome (mtDNA) carries not only well-conserved protein coding, tRNA and rRNA genes, but also highly variable non-coding regions (NCRs). However, the NCRs show poor conservation across species, making their function and evolution elusive. Identification and functional characterization of NCRs across species would be critical for addressing these questions. To this end, we devised a computational pipeline and performed de novo assembly and annotation of mtDNA from 19 Caenorhabditis species using next-generation sequencing (NGS) data. The mtDNAs for 14 out of the 19 species are reported for the first time. Comparison of the 19 genomes reveals species-specific sampling of partial displacement-loop (D-loop) sequence as a novel NCR inserted into a unique tRNA cluster, suggesting an important role of the D-loop and the tRNA cluster in shaping NCR evolution. Intriguingly, RNA-Seq analysis suggests that a novel NCR resulting from a recent duplication of NADH dehydrogenase subunit 5 (ND5) could be utilized as a 3′ UTR for up-regulation of its upstream gene. The expression analysis shows a species- and sex-specific expression of mitochondrial genes encoded by mtDNA and nucleus, respectively. Our analyses provide important insights into the function and evolution of mitochondrial NCRs and pave the way for further studying the function and evolution of mitochondrial genome.

Selfing is the safest sex for Caenorhabditis tropicalis

“…We also examined the mitochondrial genomes of JU1373 and NIC58, and found that the core functional complement is superficially identical; all 12 protein-coding, two ribosomal RNA, and 22 tRNA genes are called as present and intact in both ( Bernt et al, 2013 ; Lemire, 2005 ; Li et al, 2018 ). There are, however, several differences of unknown significance, including 12 missense variants in six of the core protein coding genes, the presence in NIC58 of a small non-coding region and a potentially novel (lowly expressed) gene encoding a 2-pass transmembrane protein, and differential expression at two additional loci ( Figure 8—figure supplement 1 ).…”

“…The inferred antagonistic Medea in NIC58 may also involve novel protein-coding potential. We also examined the mitochondrial genomes of JU1373 and NIC58, and found that the core functional complement is superficially identical; all 12 protein-coding, 2 ribosomal RNA and 22 tRNA genes are called as present and intact in both (Bernt et al, 2013;Lemire, 2005;R. Li et al, 2018).…”

Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response

“…The strategy of single strand transcription from the mitochondrial genome is not just parochial to C . elegans ; it is a strategy used by many members of the genus Caenorhabditis [ 58 ]. If the unique strand transcriptional architecture of the Caenorhabditis mitochondrial genome is linked with production of dsRNA from the mitochondria, and if the release of mitochondrial RNA into the cytosol in mitochondrial mutants is the trigger for the formation of EOL-1 foci, we would expect a suppression of EOL-1 focus formation by shutting down mitochondrial RNA biogenesis.…”

The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa

“…One of the possible reasons for the retention of gene copies and long non-coding regions in genomes is their potential functionality. For example, Li and colleagues proposed that the Nad5 -derived non-coding fragment in the Caenorhabditis briggsae mt genome upregulates the transcription of the neighboring Nad3 [ 120 ]. Transcribed copies of pseudogenes from non-coding regions of the nuclear and mt genomes were shown to participate in numerous processes of transcriptional and post-transcriptional gene regulation [ 121 , 122 ].…”