Mitochondrial DNA Research Articles

The genome sequence of the marbled rockcod, Notothenia rossii Richardson, 1844

We present a genome assembly from an individual Notothenia rossii (the marbled rockcod; Chordata; Actinopterygii; Perciformes; Nototheniidae). The genome sequence is 1,042.9 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.68 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,432 protein coding genes.

The genome sequence of lesser trefoil or Irish shamrock, Trifolium dubium Sibth. (Fabaceae)

We present a genome assembly from an individual Trifolium dubium (lesser trefoil; Tracheophyta; Magnoliopsida; Fabales; Fabaceae) as part of a collaboration between the Darwin Tree of Life and the European Reference Genome Atlas. The genome sequence is 679.1 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The two mitochondrial genomes have lengths of 133.86 kb and 182.32 kb, and the plastid genome assembly has a length of 126.22 kilobases.

The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835

We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.

Comparative Mitogenome Characterization of Cryptic Asian Seabass (Lates calcarifer) in Captivity within Peninsular Malaysia

Lates calcarifer is one of the most commercial species in the world. Yet, phylogenetic relationships among this cryptic species remain unclear despite its significance in the fishery sector. The first report on bifurcation of captive Lates calcarifer in Peninsular Malaysia (PM) inferred from complete mitochondrial genome was discussed in the present study. Two mitochondrial genomes (mitogenomes) of Lates species were sequenced and assembled. The mitogenome length was 16,627 bp and 16,515 bp for K4 and S15, respectively. The majority of PCGs in both species exhibited the common initiation marker ATG codon and ended with termination marker TAA codon. Also, the incomplete termination codon T/TA was found in both species. Most AT-skew and GC-skew values observed in the protein-coding genes (PCGs) across the two samples were negative. The phylogenetic analysis based on 13 protein-coding genes by Maximum-Likelihood tree displayed two lineages from different regions which were from Myanmar/Indian waters (K4) and Southeast Asia/ Australian waters (S15). The striking genetic distance values between both specimens indicated 13 PCGs were suffering purifying selection. This study offers significant information for future analyses of evolutionary relationships among the numerous and taxonomically puzzling perciform fishes.

Mitochondrial fractions located in the cytoplasmic and peridroplet areas of white adipocytes have distinct roles.

The role of mitochondria in white adipocytes (WAs) has not been fully explored. A recent study revealed that brown adipocytes contain functionally distinct mitochondrial fractions, cytoplasmic mitochondria, and peridroplet mitochondria. However, it is not known whether such a functional division of mitochondria exists in WA. Herein, we observed that mitochondria could be imaged and mitochondrial DNA and protein detected in pellets obtained from the cytoplasmic layer and oil layer of WAs after centrifugation. The mitochondria in each fraction were designated as cytoplasmic mitochondria (CMw) and peridroplet mitochondria (PDMw) in WAs, respectively. CMw had higher β-oxidation activity than PDMw, and PDMw was associated with diacylglycerol acyltransferase 2. Therefore, CMw may be involved in β-oxidation and PDMw in droplet expansion in WAs.

The genome sequence of black poplar, Populus nigra subsp. betulifolia L., 1753 (Salicaceae)

We present a genome assembly from an individual Populus nigra subsp. betulifola (black poplar; Tracheophyta; Malpighiales; Salicaceae). The genome sequence is 413.2 megabases in span. Most of the assembly (99.73%) is scaffolded into 19 chromosomal pseudomolecules. Mitochondrial and plastid genomes were also assembled. Three mitochondrial assemblies have lengths of 281.85, 335.57 and 186.15 kilobases, and the plastid genome has a length of 156.37 kilobases.

First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia.

We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.

Two Different Nuclear Mitochondrial DNA Mutations Associated with Retinal Abnormalities

Purpose: To report the posterior pole imaging characteristics of two patients with pathogenic nuclear mitochondrial mutations. Methods: Case reports Results: The first case, a 61-year-old patient, initially diagnosed with age-related macular degeneration, exhibited focal hyperpigmentation and increased autofluorescence in the parafoveal macula, along with geographic atrophy and mild optic nerve pallor. Optical coherence tomography (OCT) showed ellipsoid zone (EZ) attenuation, hyperreflective foci colocalizing to the hyperpigmentation, subretinal deposits, and hypertransmission defects. He was found to have a pathogenic mutation of MFN2, a gene defect associated with Charcot-Marie-Tooth disease. The second case, a 65-year-old patient presented with loss of central vision with pallor of the optic nerve. OCT imaging showed widespread loss of the interdigitation zone and EZ attenuation peripheral to the foveal region. There was thinning of the ganglion cell and nerve fiber layers. A pathogenic OPA1 mutation, the leading cause of autosomal dominant optic atrophy, was found. Both MFN2 and OPA1 produce proteins integral in mitochondrial fusion. Conclusions: The findings of these cases suggest ocular examinations may be helpful in evaluating patients with nuclear mitochondrial mutations using the near microscopic resolution of OCT. Retinal imaging may highlight structural abnormalities related to mitochondrial problems and allows direct imaging of the EZ, a layer dominated by mitochondria and a place where direct imaging of mitochondria is possible, in vivo.

Single-cell analysis reveals context-dependent, cell-level selection of mtDNA.

Heteroplasmy occurs when wild-type and mutant mitochondrial DNA (mtDNA) molecules co-exist in single cells1. Heteroplasmy levels change dynamically in development, disease and ageing2,3, but it is unclear whether these shifts are caused by selection or drift, and whether they occur at the level of cells or intracellularly. Here we investigate heteroplasmy dynamics in dividing cells by combining precise mtDNA base editing (DdCBE)4 with a new method, SCI-LITE (single-cell combinatorial indexing leveraged to interrogate targeted expression), which tracks single-cell heteroplasmy with ultra-high throughput. We engineered cells to have synonymous or nonsynonymous complex I mtDNA mutations and found that cell populations in standard culture conditions purge nonsynonymous mtDNA variants, whereas synonymous variants are maintained. This suggests that selection dominates over simple drift in shaping population heteroplasmy. We simultaneously tracked single-cell mtDNA heteroplasmy and ancestry, and found that, although the population heteroplasmy shifts, the heteroplasmy of individual cell lineages remains stable, arguing that selection acts at the level of cell fitness in dividing cells. Using these insights, we show that we can force cells to accumulate high levels of truncating complex I mtDNA heteroplasmy by placing them in environments where loss of biochemical complex I activity has been reported to benefit cell fitness. We conclude that in dividing cells, a given nonsynonymous mtDNA heteroplasmy can be harmful, neutral or even beneficial to cell fitness, but that the 'sign' of the effect is wholly dependent on the environment.

Warburg Effect Reshapes Tumor Immunogenicity.

Tumor cells rewire their metabolism to fulfill the demands of highly proliferative cells. This changes cellular metabolism to adapt to fuel and oxygen availability for energy production and to increase the synthesis capacity of building blocks for cell division and growth. In addition, the metabolic shift also modulates the immunogenicity of the tumor cells. Recently, Mahmood and colleagues reported a connection between mitochondrial DNA mutations in cancer cells and their response to immunotherapy in a mouse model of melanoma.

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae.

Angelica dahurica is a kind of Chinese traditional herbs with economic and ornament value, widely distributed in China. Despite its significance, there have been limited comprehensive investigations on the genome of A. dahurica, particularly regarding mitochondrial genomes. To investigate the conversion between mitochondrial genome and chloroplast genome, a complete and circular mitochondrial genome was assembled using Oxford Nanopore Technologies (ONT) long reads. The mitochondrial genome of A. dahurica had a length of 228,315 base pairs (bp) with 45.06% GC content. The mitochondrial genome encodes 56 genes, including 34 protein-coding genes, 19 tRNA genes and 3 rRNA genes. Moreover, we discovered that 9 homologous large fragments between chloroplast genome and mitochondrial genome based on sequence similarity. This is the first report for A. dahurica mitochondrial genome, which could provide an insight for communication between plastid genome, and also give a reference genome for medicinal plants within the Angelica family.

A new shallow water species of the palaemonid shrimp genus Palaemon Weber, 1795 (Decapoda: Caridea) from Japan

During a survey of the shallow water decapod fauna in the Miura Peninsula, Kanagawa Prefecture, central Japan, four specimens of a new palaemonid shrimp, Palaemon parvibrachium n. sp., were collected from sea grass beds of Nanozostera japonica (Ascherson & Graebner) Tomlinson & Posluszny, 2001. The new species appears morphologically similar to P. serrifer (Stimpson, 1860), one of the most common representatives of Palaemon Weber, 1795 in Japanese waters, but the short carpus of the second pereopod and the different live colouration readily differentiate the new species from the latter. A DNA barcode (a partial fragment of the mitochondrial CO1 gene), as well as a partial fragment of the mitochondrial 16S rRNA gene, are provided to genetically characterize the new species.

The genome sequence of a false flower beetle, Anaspis maculata (Geoffroy in Fourcroy, 1785)

We present a genome assembly from an individual female Anaspis maculata (false flower beetle; Arthropoda; Insecta; Coleoptera; Scraptiidae). The genome sequence is 757.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,965 protein coding genes.

Gapless assembly of Babesia bovis NVSL348.

We are reporting a Babesia bovis genome containing four nuclear chromosomes, a mitochondrial genome, and an apicoplast from reference isolate NVSL348. This report includes a gapless assembly consisting of all six genetic molecules.

The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839)

We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.

The genome sequence of the beech bark beetle, Taphrorychus bicolor (Herbst, 1793)

We present a genome assembly from an individual male Taphrorychus bicolor (the beech bark beetle; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence is 575.2 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,125 protein coding genes.

The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766)

We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.

Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii.

The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P.drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.

Cell-Free Nuclear and Mitochondrial DNA as Potential Biomarkers for Assessing Sepsis Severity

Sepsis continues to be a significant public health challenge despite advances in understanding its pathophysiology and management strategies. Therefore, this study evaluated the value of cell-free nuclear DNA (cf-nDNA) and cell-free mitochondrial DNA (cf-mtDNA) for assessing the severity and prognosis of sepsis. Ninety-four patients were divided into three groups: infection (n = 32), sepsis (n = 30), and septic shock (n = 32). Plasma samples were collected at the time of diagnosis, and cfDNA concentrations were determined by qPCR assay. The results showed that plasma cfDNA levels increased with the severity of the disease. To distinguish between patients with infection and those with sepsis, the biomarker L1PA290 achieved the highest AUC of 0.817 (95% CI: 0.725–0.909), demonstrating a sensitivity of 77.0% and a specificity of 79.3%. When cf-nDNA was combined with the SOFA score, there was a significant improvement in the AUC (0.916 (0.853–0.979)), sensitivity (88.1%), and specificity (80.0%). Moreover, patients admitted to the ICU after being diagnosed with sepsis had significantly higher cf-nDNA concentrations. In patients admitted to the ICU, combining cf-nDNA with the SOFA score yielded an AUC of 0.753 (0.622–0.857), with a sensitivity of 95.2% and a specificity of 50.0%. cfDNA can differentiate between patients with infection and those with sepsis. It can also identify patients who are likely to be admitted to the ICU by predicting those with indications for intensive care, suggesting its potential as a biomarker for sepsis.

Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.