Mitochondrial DNA Research Articles

Aberrant fragmentomic features of circulating cell-free mitochondrial DNA as novel biomarkers for multi-cancer detection.

Fragmentomic features of circulating cell free mitochondrial DNA (ccf-mtDNA) including fragmentation profile, 5' end base preference and motif diversity are poorly understood. Here, we generated ccf-mtDNA sequencing data of 1607 plasma samples using capture-based next generation sequencing. We firstly found that fragmentomic features of ccf-mtDNA were remarkably different from those of circulating cell free nuclear DNA. Furthermore, region-specific fragmentomic features of ccf-mtDNA were observed, which was associated with protein binding, base composition and special structure of mitochondrial DNA. When comparing to non-cancer controls, six types of cancer patients exhibited aberrant fragmentomic features. Then, cancer detection models were built based on the fragmentomic features. Both internal and external validation cohorts demonstrated the excellent capacity of our model in distinguishing cancer patients from non-cancer control, with all area under curve higher than 0.9322. The overall accuracy of tissue-of-origin was 89.24% and 87.92% for six cancer types in two validation cohort, respectively. Altogether, our study comprehensively describes cancer-specific fragmentomic features of ccf-mtDNA and provides a proof-of-principle for the ccf-mtDNA fragmentomics-based multi-cancer detection and tissue-of-origin classification.

The genome sequence of a woodlouse fly, Melanophora roralis (Linnaeus, 1758)

We present a genome assembly from an individual female woodlouse fly, Melanophora roralis (Arthropoda; Insecta; Diptera; Rhinophoridae). The genome sequence has a total length of 565.10 megabases. Most of the assembly (98.9%) is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 19.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,321 protein-coding genes.

The genome sequence of Pearl Grass-veneer, Catoptria pinella Linnaeus, 1758

We present a genome assembly from an individual male Catoptria pinella (pearl grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 386.90 megabases. Most of the assembly (99.77%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,308 protein-coding genes.

The genome sequence of a true bug, Aradus depressus (Fabricius, 1794)

We present a genome assembly from an individual male true bug, Aradus depressus (Arthropoda; Insecta; Hemiptera; Aradidae). The genome sequence has a total length of 697.70 megabases. Most of the assembly (98.69%) is scaffolded into 14 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.81 kilobases in length.

Visual analysis of postmortem interval estimation trends and collaborative networks: a 15-year study (2006-2020).

Utilizing a visual analysis of the literature on postmortem interval (PMI) estimation indexed by Web of Science (WOS), this study investigates developmental trends and research hot points across each 5-year period from 2006 to 2020. Additionally, collaborative efforts among authors, countries, and institutions were examined. Research hot points, high-frequency keywords, authors, countries and institutions in relevant papers were analyzed using CiteSpace.5.7.R2 information visualization analysis software over the past 15 years. The literature related to PMI estimation has witnessed consistent growth over time. In the keyword co-occurrence network, several impactful terms stand out, including blowfly, mitochondrial DNA, and emerging concepts like virtual autopsy. Technological advancements, such as RNA stability analysis and virtual autopsy tools, have played a pivotal role in shaping the direction of PMI research. Scientific research institutions dominate the high-frequency affiliations within the institutional cooperative network. Additionally, the country cooperative network exhibits a trend of co-occurrence and multi-clustering. As science and technology continue to advance, traditional PMI estimation methods mature while novel interdisciplinary approaches drive innovation. By identifying emerging trends and research hotspots, this study provides a roadmap for future investigations, guiding researchers toward new opportunities in PMI estimation.

Evaluation of β-Actin and Mitochondrial DNA Levels in Determining the Age of Suidae Remains.

African Swine Fever (ASF) is an infectious disease affecting pigs and wild boars, causing significant economic losses. Epidemiological surveillance plays an important role in minimizing its impact. The aim of this study was to evaluate the usefulness of β-actin DNA and mitochondrial DNA (mtDNA) levels in determining the age of animal remains from the Suidae family, which could be helpful in epidemiological investigations. The study included selected tissues and internal organs of Sus scrofa domesticus, exposed to natural environmental conditions or kept in stable 4 °C conditions, to assess the levels of β-actin and mtDNA over a period of 18 months. The levels of both tested parameters exhibited the expected decreasing trend over time. However, in most tissues, some discrepancies from this general pattern were observed. The results obtained for bone marrow showed a consistent downward trend and a strong correlation between mtDNA and β-actin, with long-term detectability (up to the 13th month of the study). Therefore, bone marrow could be considered a matrix of choice for age assessment. However, due to various influencing factors, further studies are required.

Description of a new species of the Asian newt genus Tylototriton (Amphibia, Urodela, Salamandridae) from Hunan Province, China

The newt genus Tylototriton is widely distributed in east, southeast, and south Asia. Previous studies have shown that basic surveys of this genus are far from comprehensive, and unknown species still exist within the group. In this study, we described a new species of this genus, Tylototriton gaowangjienensissp. nov., from Gaowangjie National Nature Reserve in Hunan Province, China, based on evidence from molecular identification and morphological comparisons. Additionally, we conducted phylogenetic analysis of the genus to elucidate the taxonomic status of the new species. Based on combined mitochondrial 16S rRNA and ND2 gene sequences, the phylogenetic tree supported the new species as a member of the T. wenxianensis species subclade in the subgenus Yaotriton. It can be distinguished from its congeners by the combination of the following characteristics: (1) medium-sized body; (2) finger tips extending beyond the snout while forelimbs stretched forward; (3) tips of forelimbs and hindlimbs reaching and overlapping when folded towards the body; (4) snout edge round; (5) absence of small papillae in the male cloacal fissure; (6) dorsal ridges narrow, with width smaller than the eye diameter; (7) head length (HDL) greater than head width (HDW) (HDL/HDW = 1.04~1.22); (8) orange markings absence on the parotoid; (9) nodule-like warts on body sides continuous; (10) vomerine teeth not connected at the tip, extending to the occipital bone at the posterior end.

First Record of Aphelenchoides oryzae on Foxtail Millet (Setaria italica (L.) P. Beauv.) in Jilin Province of China.

Aphelenchoides oryzae Yokoo caused a large reduction in rice yields in Japan (1948). It was later synonymised with A. besseyi by Allen (1952), but Subbotin et al. (2021) considered it a valid species. In the main foxtail millet (Setaria italica (L.) P. Beauv.) production area of western Jilin Province, China, many plants were stunted, with thin spikes and open, smooth, shiny glumes. Severely affected spikes were noticeably shorter, fluffy at the top, and erect. In August 2023, 10 foxtail millet samples were collected and nematodes were isolated from 9 of them. A population from Songyuan City, Jilin Province (E:123.64, N:44.86) was studied. The average number of nematodes isolated per gram of ear was 510.7 ± 15.17. Female body slender, lip region rounded, lateral fields with 4 or 6 incisures, vulva located at 71.6% of the body length, post vulvar uterine sac (PUS) 3.7 times anal body width long but less than quarter distance from vulva to anus (VA), tail conical with 3 or 4 terminal spikes. The body length (L), maximum body width (W) and tail length of the female (mean, n=25) were 648 μm, 15.9 μm and 36.7 μm, respectively. PUS length / (VA)% = 23.5, L/W = 41.1, L/ tail length = 17.8. Male body tail curves like a sickle, lacks bursa and shows three pairs of copulatory papillae. Spicules typical of the genus except that the proximal end lacks a dorsal process and has only a moderately developed rostrum. Male measured (mean, n = 25): L = 525.8 μm, W = 14.8 μm, tail length = 34.0 ± 0.7 μm, spicule length = 16.4 μm; L/W = 35.6; L/tail length = 15.6 μm. Amplification of the D2-D3 expansion segments of the 28S ribosomal RNA and the cytochrome oxidase subunit I (COI) gene of mitochondrial DNA (mtDNA) with primers the forward D2A (5'-ACAAGTACCGTGAGGGAAAGTTG-3') and the reverse D3B (5'-TCGGAAGGAACCAGCTACTA-3') (Subbotin et al. 2006), and forward COI-F1 (5'-CCTACTATGATTGGTGGTTTTGGTAATTG-3') and the reverse COI-R2 (5'-GTAGCAGCAGTAAAATAAGCACG-3') (Kanzaki and Futai 2002). PCR conditions were as described by Ye et al. (2007). The sequences of 28S D2-D3 region (726 bp, PP573753- PP573761) of rDNA were 100% identical to A. oryzae (KY123700, KY123694) and COI region (698-700 bp, PP733171-PP733179), were 98.88% identical to A. oryzae (GU367867). Bayesian inference was used to construct phylogenetic tree of 28S D2-D3 region and COI gene, which showed that the Jilin populations clustered together with A. oryzae, which was a sister branch of A. besseyi. Pathogenicity was established via the infection of foxtail millet (cv. Jiyou 2). The germinated foxtail millet seeds were planted in pots containing 350 ml of sterile soil mixture. On the 15th day, every 10 seedlings were inoculated with 100 A. oryzae at the leaf sheet wounds and 3 plants were noninoculated as control. Three independent replicates were performed on different dates. Forty days post-inoculation, an average of 88.3 ± 2.26 A. oryzae were extracted from each nematode-inoculated plant, and the plants were yellowed and necrotic, uninoculated plants grew normally. The molecular and morphological identification of the nematodes obtained by re-isolation from the plants was identical to that of A. oryzae. Our findings clarify the pathogen species, which can be targeted to develop prevention and control strategies, which are important for ensuring safe grain production and helping promote sustainable local agricultural production. To our knowledge, this is the first record of A. oryzae on foxtail millet in Jilin, China.

Maternal mitochondrial DNA copy number and methylation as possible predictors of pregnancy outcomes in a Michigan pregnancy cohort

ABSTRACT Background: Little is understood about the role of mitochondria in pregnancy-related adaptations. Therefore, we evaluated associations of maternal early-to-mid pregnancy mitochondrial DNA copy number (mtDNAcn) and mtDNA methylation with birth size and gestational length. Methods: Michigan women (n=396) provided venous bloodspots at median 11 weeks gestation to quantify mtDNAcn marker NADH-ubiquinone oxidoreductase chain 1 (ND1) using real-time quantitative PCR and mtDNA methylation at several regions within four mitochondria-specific genes using pyrosequencing: MTTF (mitochondrially encoded tRNA phenylalanine), DLOOP (D-loop promoter region, heavy strand), CYTB (cytochrome b), and LDLR (D-loop promoter region, light strand). We abstracted gestational length and birthweight from birth certificates and calculated birthweight z-scores using published references. We used multivariable linear regression to evaluate associations of mtDNAcn and mtDNA methylation with birthweight and birthweight z-scores. Cox Proportional Hazards Models (PHMs) and quantile regression characterized associations of mitochondrial measures with gestational length. We also considered differences by fetal sex. Results: Using linear regression and Cox PHMs, mtDNAcn was not associated with birth outcomes, whereas associations of mtDNA methylation with birth outcomes were inconsistent. However, using quantile regression, mtDNAcn was associated with shorter gestation in female newborns at the upper quantiles of gestational length, but with longer gestational length in males at the lower quantiles of gestational length. Maternal LDLR, DLOOP, and MTTF methylation was associated with longer gestational length in females at the upper quantiles and in males at lower gestational length quantiles. Conclusions: Maternal mtDNAcn and mtDNA methylation were associated with gestational length in babies born comparatively early or late, which could reflect adaptations in mitochondrial processes that regulate the length of gestation.

The genome sequence of the rose sawfly Arge pagana Linnaeus, 1758

We present a genome assembly from a female specimen of Arge pagana (large rose sawfly; Arthropoda; Insecta; Hymenoptera; Argidae). The genome sequence has a total length of 204.70 megabases. Most of the assembly (94.4%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 26.8 kilobases in length.

The genome sequence of the alder spittlebug, Aphrophora alni (Fallén, 1805)

We present a genome assembly from an individual male Aphrophora alni (the alder spittlebug; Arthropoda; Insecta; Hemiptera; Aphrophoridae). The genome sequence has a total length of 1,781.50 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 27.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,940 protein-coding genes.

The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822)

We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.

The genome sequence of a braconid wasp, Zele albiditarsus Curtis, 1832

We present a genome assembly from a female braconid wasp, Zele albiditarsus (Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence has a total length of 137.70 megabases. Most of the assembly (99.98%) is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 23.96 kilobases in length.

The “evolution” of the mitochondrial genome of the (<i>Phylloscopus borealis</i> sensu lato) occurs in its nuclear genome

Sequencing of a partial fragment of the ND5–cytb mithochondrial genes (1553 bp) and its nuclear copies was carried out to Phylloscopus borealis sensu lato, belonging to individual taxonomic groups from different parts of the range. It was shown that the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms were identical to those in nuclear copies of borealis mtDNA. Differences between mitochondrial haplotypes of examinandus and nuclear copies of mtDNA borealis were low (p = 0.02), at the same time the mtDNA genetic divergence in borealis–examinandus, borealis–xanthodryas and examinandus–xanthodryas significantly exceeded this value (p = 0.035, 0.044 and 0.046, respectively). A nuclear copy of the mitochondrial haplotype of the easternmost form of xanthodryas was first discovered in the nuclear genome of one borealis individual in the western part of the breeding range (Komi Republic). Alongside this, it was shown at the first time, the nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were close to the mitochondrial haplotypes of borealis from Kytlym (Sverdlovsk region) (p = 0.018). Thus, the mutations emerging in the nuclear copies of mitochondrial genes are the source of most substitutions in the mitochondrial DNA of the studied forms. The origin of the mitochondrial haplotypes examinandus and xanthodryas from nuclear copies of mtDNA borealis and the close similarity of their nuclear genomes gives grounds to consider the mitogenomes of these forms as variants of the haplotype of the single species Ph. borealis sensu lato. With a high degree of probability, it can be argued that the divergence time of the haplotypes of the analyzed forms is significantly less than 2.5-3 million years, as previously assumed by a number of authors [Saitoh et al. 2010; Alström et al. 2011], and the “molecular clock” that do not take into account recombination events between the nuclear and mitochondrial genomes cannot be used in this case.

The genome sequence of the Cinerous Pearl moth, Anania fuscalis (Denis & Schiffermüller) 1775

We present a genome assembly from an individual female Anania fuscalis (the cinerous pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence spans 563.90 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,765 protein-coding genes.

The genome sequence of Hoary Whitlowgrass, Draba incana L.

We present a genome assembly from a specimen of Draba incana (Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence has a total length of 667.80 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2n = 32). The mitochondrial and plastid genome assemblies have lengths of 283.08 kilobases and 153.57 kilobases, respectively.

The genome sequence of cowslip, Primula veris L.

We present a genome assembly from a specimen of Primula veris (Streptophyta; Magnoliopsida; Ericales; Primulaceae). The genome sequence has a total length of 436.20 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 326.21 kilobases and 153.48 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 26,584 protein-coding genes.

Diving deeper into the taxonomy of the Neoscopelus species complex (Myctophiformes: Neoscopelidae) with the description of Neoscopelus serranoi sp. nov.

Previous studies have highlighted possible cryptic biodiversity in the genus Neoscopelus. This hypothesis was tested using new morphological, molecular and biogeographical data on species of this genus caught in the north Atlantic between 2010 and 2022. The information obtained has been combined with available data in an integrative approach, including a review of morphological characters reported in the ichthyological literature and DNA-based species delimitation analyses. The main outcome of the present study is the description of Neoscopelus serranoi sp. nov. from the Atlantic and southwestern Indian Oceans. The new species is morphologically very similar to Neoscopelus microchir from which differs in having a shorter anal-fin base, a shorter pelvic fin, more dorsal and pectoral-fin rays, less anal-fin rays, fewer gillrakers and fewer isthmus and lateral photophores. They also differ in geographic distribution, with the new species occurring in the Atlantic Ocean and the near southwestern Indian Ocean, whereas N. microchir was originally described from Japanese waters of the Pacific Ocean. A literature review of available morphological data between geographic areas for Neoscopelus macrolepidotus and Neoscopelus microchir showed a large intraspecific overlap and no boundaries. However, molecular species delimitation based on the mitochondrial COI gene revealed the existence of cryptic diversity in both species, with eight to ten molecular operational taxonomic units (MOTU), compared to three valid species. Neoscopelus serranoi sp. nov. was considered an independent MOTU in all analyses performed, supporting the morphological identification as a new species. These results highlight that the taxonomy of Neoscopelus is far from settled and show that a greater sampling effort is needed to resolve the uncertainties and to describe unknown putative species. This also exemplifies the virtues of integrative taxonomy in delving into the systematics of deep-sea fishes.

The Complete Mitochondrial Genome of Nephropsis grandis: Insights into the Phylogeny of Nephropidae Mitochondrial Genome.

The systematic phylogeny of Pleocyemata species, particularly within the family Nephropidae, remains incomplete. In order to enhance the taxonomy and systematics of Nephropidae within the evolutionary context of Pleocyemata, we embarked upon a comprehensive study aiming to elucidate the phylogenetic position of Nephropsis grandis. Consequently, we determined the complete mitochondrial DNA sequence for N. grandis. The circular genome spans a length of 15,344bp and exhibits a gene composition analogous to that observed in other metazoans, encompassing a comprehensive set of 37 genes. Additionally, the genome features an AT-rich region. The rRNAs exhibited the highest AT content among the 37 genes (70.41%), followed by tRNAs (67.42%) and protein-coding genes (PCGs) (62.76%). The absence of a dihydrouracil arm in trnS1 prevented the formation of the canonical cloverleaf secondary structure. Selective pressure analysis indicated that the PCGs underwent purifying selection. The Ka/Ks ratios for cox1, cox2, cox3, and cob were considerably lower compared to other PCGs, implying strong purifying selection acting upon these particular genes. The mitochondrial gene order in N. grandis was consistent with the reported order in ancestral Pleocyemata. Phylogenetic revealed that N. grandis forms a cluster with the genus Metanephrops, and this cluster further groups with Homarus and the genus Nephrops within the Nephropidae family. These findings provide robust support for N. grandis as an ancestral member of the Nephropidae family. This study highlights the significance of employing complete mitochondrial genomes in phylogenetic analysis and deepens our understanding of the evolution of the Nephropidae family.

Exploring mitochondrial blood-based and genetic markers in older adults with mild cognitive impairment and remitted major depressive disorder

Mild cognitive impairment (MCI) is a prodromal stage in aging to possible progression to Alzheimer’s disease and related dementia (ADRD), where co-occurrence of major depressive disorder (MDD) accelerates the progression. Metabolic and mitochondrial abnormalities in ADRD and other neurodegenerative disorders have been widely suggested, while possible mitochondrial dysfunction has been associated with etiopathology of both MCI and MDD. Hence, investigation of mitochondrial markers in MCI, MDD, and presence of both conditions is warranted. In total, 332 older adult participants were included: 168 with MCI, 108 with MCI plus remitted MDD (rMDD), and 56 with rMDD but without MCI. We measured plasma circulating mitochondrial DNA (ccf-mtDNA), lactate, and extracted nuclear mitochondrial encoded (NMt) single-nucleotide variants (SNVs) (n = 312). Non-parametric statistical tests on ccf-mtDNA and lactate levels were performed on the diagnosis, clinical and cardiometabolic variables. Binary sequence kernel association test (SKAT-O) and burden test were performed on NMt-SNV, adjusted for age, race, gender, type II diabetes, and APOE genotype. Lower level of lactate was observed in MCI (KW χ2 = 14.8, P = 0.0024), more specifically, significant differences of lower plasma lactate between MCI only and rMDD, but not between MCI+rMDD and MCI were found, suggesting potential roles in MCI driving lactate lower levels. While higher levels of ccf-mtDNA were observed in APOE-ε4 carrier (χ2 = 5.04, P = 0.05). This relationship was present only in MCI (P = 0.043) and MCI+rMDD groups (P = 0.023). No significant nuclear-encoded mitochondrial gene associations were observed with MCI or MDD. The results suggest decreased level of plasma lactate in individuals with MCI and MCI+rMDD, with inverse correlation with ccf-mtDNA, in addition to effect of APOE-ε4 in further increasing ccf-mtDNA specifically in participants with cognitive impairment. These findings contribute to a deeper understanding of the mitochondrial markers in MCI and MDD, warranting further research to explore the precise roles of mitochondrial abnormalities in the development and progression of MCI.