ATP6 Gene Research Articles

Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma

Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93–92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.

Phylogenetic Study of Several Parasitic Plant Species Based on The atp-1 Gene Sequence

The distinction between parasitic and non-parasitic plants can be determined by analyzing the atp-1 gene, which plays a vital role in respiration and is known for its high mutation rate. This study analyzed the kinship of parasitic plant subclass species through the construction of a phylogenetic tree based on atp-1 gene sequences. The atp-1 gene sequences of parasitic and non-parasitic plants with a total of 29 species were obtained from NCBI. The sequences were then aligned with ClustalW and analyzed for mutation patterns. Sequences that have been aligned, phylogenetic trees were made with MEGA11 software with the Maximum Likelihood method and analyzed using the iTOL website. The sequences were analyzed for similarity and kinship with Matrix Coefficient and Haplotype Construction. The atp-1 gene proved that parasitic plants (hemiparasites) are furthermore related to non-parasitic plants compared to holoparasite parasitic plants. Besides that, the kinship of parasitic plants can be analyzed by several methods, namely matrix coefficient to measure similarity, DnaSP to analyzing haplotype, and haplotype network to find out detailed information on mutations that occur. Matrix coefficients can also be used to measure specific similarities between species. It was found that the same subclass had high similarities, for example the species Santalum album and Heisteria parvifolia with a genetic distance value of 0.00574. Meanwhile, different subclasses have low similarity, such as Cassytha filiformis and Ombrophytum with a genetic distance value of 0.07871. This study shows that the atp-1 gene is effective in analyzing the kinship between parasitic and non-parasitic plants. Hemiparasites are genetically closer to non-parasitic plants than holoparasites, with higher genetic similarity within the same subclass.

Characterization of mitochondrial DNA mutations in colorectal cancer progression by in silico approach and use as potential biomarkers for diagnosis and prognosis

BackgroundMitochondrial DNA variants are significant contributors to cancer progression, as evidenced by numerous findings. This study focuses on characterizing mitochondrial DNA mutations in colorectal cancer progression and their potential as biomarkers.MethodologyNext generation sequencing technology was employed to analyze mitochondrial DNA variants in tumor and adjacent normal tissues from 25 patients with colon/rectal cancer. In silico prediction tools (SIFT, Polyphen2, Mutation Assessor, and SNP&GO) were utilized to assess the pathogenicity of these variants. Additionally, homology modeling of mutated protein structures was conducted, and molecular dynamic simulations were performed to assess the impact of mutation on protein function.ResultsEighteen variants were identified across most tumor tissue samples, located in genes from Complex I, IV, and V. Among the identified variants, the V302M and S461 mutations in the MT-ND5 gene and L137F and L220P mutations in the ATP6 gene were predicted to be deleterious, potentially affecting protein function. 3D structural analysis of both wild-type and mutant proteins of MT-ND5 revealed changes in flexibility for the V302M and S461G mutations. The MT-ATP6 mutations L135F and L220P disrupt the interactions with surrounding residues and affect the overall function of protein. Further changes in protein dynamics of the mutated proteins by molecular dynamic simulations also indicate the effects; the mutations have on protein function.ConclusionMT-ND5 and MT-ATP6 variants could serve as potential biomarkers and drug targets in colorectal cancer. This study underscores the significance of mitochondrial DNA variants in cancer progression.

Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini)

Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.

Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China

BackgroundThe sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the “Queen of the Tea Family”, most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.ResultsIn this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836 bp (C. nitidissima) to 1,098,121 bp (C. tianeensis) with GC content of 45.71–45.78% and contained 48–58 genes, including 28–37 protein-coding genes, 17–20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.ConclusionsIn this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.

Characterization of the Complete Mitochondrial Genome of Pleurogenoides japonicus (Digenea, Pleurogenidae): Comparison With the Members of Microphalloidea and Phylogenetic Implications.

Pleurogenoides japonicus (Trematoda: Microphalloidea) is an important parasite in wood frogs with high infection rates and significant ecological, economic, and societal importance. The scarcity of molecular data for these parasites severely limits population genetics and phylogenetic studies. In the present study, for the first time, we determined and described the entire mitochondrial (mt) genome of P. japonicus as the first representative of the family Pleurogenidae. The entire mt genome of P. japonicus was circular, with 15,043 bp (GenBank accession number OR900118), containing 36 genes, comprising 12 protein-coding genes (cox1-3, nad1-6, nad4L, cytb, and atp6), two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions. There were 23 intergenic spacers, ranging from 2 to 162 bp, and only one 40 bp overlap between nad4L and nad4 genes in the P. japonicus mt genome. The nucleotide composition of P. japonicus mt genome exhibited a strong AT bias with a 63.75% A + T content, while the AT- and GC-skews were - 0.435 and 0.407, respectively. Comparative analysis demonstrated that the P. japonicus mt genome shared the most common characteristics with Microphalloidea trematodes, and the cox1 gene was the longest and most conserved gene in Microphalloidea trematodes. The gene arrangements of Xiphidiata trematodes were of the same order based on protein-coding genes and rRNA genes, except for tRNA. More than two gene arrangement types exist in Echinostomata and Xiphidiata, and the gene rearrangement events mainly occurred in "trnE-trnG" and "trnG-trnE". Phylogenetic analysis suggested that trematodes of the family Pleurogenidae clustered more with Prosthogonimidae than Eucotylidae. The mt genome data of P. japonicus provide an accurate genetic marker for further studies of Xiphidiata trematodes.

A new species of alien land flatworm in the Southern United States.

Specimens of a flat and dark brown land planarian were found in a plant nursery in North Carolina, USA in 2020. On the basis of examination of photographs of the live specimens only, the specimens were considered as belonging to Obama nungara, a species originally from South America, which has now invaded a large part of Europe. Unexpectedly, a molecular analysis revealed that the specimens did not belong to this species, neither to the genus Obama. We then undertook its histological study, which finally confirmed that the species is a member of the genus Amaga: the species is herein described as a new species, Amaga pseudobama n. sp. The species has been found in three locations in North Carolina and some infested plants were from Georgia. We reinvestigated specimens collected in Florida in 2015 and found that they also belong to this species. Citizen science observations suggest its presence in other states. Therefore, it is likely that A. pseudobama has already invaded a part of south-east USA and that the invasion took place more than ten years ago. The complete 14,909 bp long mitochondrial genome was obtained. The mitogenome is colinear with those of other Geoplanidae and it was possible to find and annotate a tRNA-Thr, which has been reported missing in several geoplanids. Amaga pseudobama shares with other Geoplaninae the presence of alternative start codons in three protein-coding genes of its mitogenome. The availability of this new genome helped us to improve our annotations of the ND3 gene, for which an ATT start codon is now suggested. Also, the sequence of the ATP6 gene raised questions concerning the use of genetic code 9 to translate the protein-coding genes of Geoplanidae, as the whole translated protein would not contain a single methionine residue when using this code. Two maximum likelihood phylogenies were obtained from genomic data. The first one was based on concatenated alignments of the partial 28S, Elongation Factor 1-alpha (EF1) and cox1 genes. The second was obtained from a concatenated alignment of the mitochondrial proteins. Both strictly discriminate A. pseudobama from O. nungara and instead associate it with Amaga expatria. We note that the nine species currently accepted within Amaga can be separated into two groups, one with extrabulbar prostatic apparatus, including the type species A. amagensis, and one with intrabulbar prostatic apparatus, including the new species A. pseudobama. This suggests that species of the latter group should be separated from Amaga and constitute a new genus. This finding again illustrates the possible emergence of new invasive species in regions naturally devoid of large land planarians, such as North America. Amaga pseudobama thus deserves to be monitored in the USA, although its superficial resemblance to O. nungara and Geoplana arkalabamensis will complicate the use of photographs obtained from citizen science. Our molecular information provides tools for this monitoring.

Whole Mitochondrial Genome Sequencing Analysis of Canine Testicular Tumours.

Currently, the molecular background based on mitochondrial DNA (mtDNA) analysis of canine testicular tumours is underestimated. The available data mostly focus on histopathological evaluations, with a few reports of nuclear genome (nDNA) studies. Tumourigenesis represents a highly complex and diverse genetic disorder, which can also encompass defects in mtDNA. The aim of this study was to identify molecular changes in whole mitochondrial genome sequences obtained from dogs affected by testicular tumours. Samples of blood, tumour, and healthy tissue were collected from each animal, and mtDNA (ultimately 45 samples) was subsequently sequenced. Thereafter, protein analyses were performed to assess the impact of the identified molecular alterations on the amino acid level. The total number of observed changes included 722 SNPs, 12 mutations, 62 indels, 5 indel mutations, and 35 heteroplasmic sites. The highest number of mtDNA variants in protein-coding genes COX1, COX3, ATP6, ND1, ND4, and ND5 was observed. Interestingly, SNPs were found in 10 out of 22 tRNA genes. Most of the identified mtDNA defects were synonymous changes at the amino acid level. Also, polymorphisms and heteroplasmy were frequently observed in the variable number of tandem repeat (VNTR) regions, especially in its fragment spanning 16,138-16,358 bp. Based on the obtained results, it was possible to select 11 polymorphisms that occurred in all the tested samples (benign, malignant) and an additional five SNPs identified only in benign neoplasms. The comprehensive analysis of malignant testicular tumours demonstrated a significant diversity in their molecular profiles, with changes ranging from 17 to 101 per sample.

Optimizing growth and mitochondrial function in rainbow trout, Oncorhynchus mykiss through eco-friendly dietary and changes in water temperature regimen strategies

Developing sustainable aquaculture remains a challenge, notably finding suitable alternatives to marine ingredients in carnivorous fish diets such as rainbow trout (Oncorhynchus mykiss) in changing climate. These new diets are especially important because rainbow trout are an ecologically and economically significant aquaculture species. Therefore, we investigated the impact of sustainable ingredients and water temperature manipulations on rainbow trout growth characteristics and mitochondrial function. A total of 432 fish were fed four isocaloric, isolipidic, and isonitrogenous diets comprised 40 % crude protein and 20 % lipid and formulated as diet 1 (animal-based protein +25 % fish oil/ 50 % plant oil/ 25 % terrestrial animal oil), or diet 2 (animal-based protein +100 % plant oil), or diet 3 (plant-based protein +25 % fish oil/ 50 % plant oil/25 % terrestrial animal oil), or diet 4 (plant-based protein +100 % plant oil) at 14 °C or 18 °C or 20 °C water temperature. Results showed percent weigh gain (PWG) and specific growth rate (SGR), feed efficiency (FE), and feed intake (FI) were significantly (P < 0.05) higher in fish reared at 14 °C and 18 °C compared to 20 °C. The PWG, FE, FI, and SGR levels were significantly (P < 0.05) higher for fish fed diets 1 and 2 than those fed diets 3 and 4. Dietary composition influenced whole-body proximate composition, while temperature affected protein, moisture, and lipid contents. For protein, lipid, and energy contents, temperature-diet interactions were significant (P < 0.05). There were differences in mitochondrial enzymatic activities in muscle, liver and intestine. Diet affected only complex V activity in the liver, whereas temperature significantly (P < 0.05) affected the activities of complexes II, III, and V. A temperature-dietary interaction was observed for complex V. The temperature regimens, but not dietary composition, affected muscle mitochondrial enzymatic activities. There were significant (P < 0.05) effects of temperature on complex III, IV, and citrate synthase activities in the intestine, whereas dietary composition had no significant impact (P > 0.05). Based on diet, temperature, and diet-temperature interactions effects, selected genes were expressed differently in different tissues. The nd1, cox2, cytb, cox1, atp6 and PPAR-α genes were significantly influenced by diet and temperature interactions in muscle, liver and intestine. Overall, our results showed that both temperature and dietary composition had significant effects on growth characteristics, proximate composition, mitochondrial enzymatic activities, and their interactions on gene expression levels in rainbow trout. These findings underscore the importance of considering these factors in the development of plant-based aquafeeds in order to optimize growth and productivity.

Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae).

(1) Background: Mitochondrial genomes have been extensively employed as a crucial marker in numerous dipteran families for understanding phylogenetics and systematics relations, thereby playing a pivotal role in molecular biology studies. The phylogenetic relationship of the Harnischia generic complex remains contentious due to the paucity of taxonomic and molecular data. Specifically, the evolutionary relationships among Cryptochironomus, Demicryptochironomus, and Harnischia are still unclear. (2) Methods: In this study, Polypedilum and Endochironomus were used as outgroups to analyze phylogenetic relationships among Cryptochironomus, Demicryptochironomus, and Harnischia, mitogenomes of four Cryptochironomus, two Demicryptochironomus, two Harnischia, and two Cladopelma were newly sequenced. Subsequently, we conducted a thorough analysis of the nucleotide composition, sequence length, and evolutionary rate. (3) Results: All mitogenomes exhibited structural conservation, with all genes consistently arranged in the identical order as that of the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein-coding genes undergo rigorous purification selection, with the ATP8 gene exhibiting the most rapid evolutionary rate among them. Utilizing Bayesian Inference (BI) and Maximum Likelihood (ML) methods across various databases, we reconstructed the phylogenetic relationships among the genera within the Harnischia generic complex, drawing insights from an analysis of 14 mitochondrial genomes. (4) Conclusions: Our results showed that the monophyly of the genera Harnischia was well supported in all topologies; Cryptochironomus is sister to Demicryptochironomus.

Mutational analyses of mitochondrial ATP6 gene reveal a possible association with abnormal levels of lactic acid and ammonia in Bangladeshi children with autism spectrum disorder: A case-control study

Autism spectrum disorder (ASD) is a multifactorial and highly heterogeneous neurodevelopmental disorder. Mitochondrial dysfunction, caused by the genetic variations in the electron transport chain (ETC) complexes and marked by higher lactic acid and ammonia levels, can play a crucial role in the development of autism. This study focused on identifying genetic variants in the mitochondrial ATP6 gene of children with ASD and their association with autism disease outcome, disease severity, lactic acid and ammonia levels. Ninety children were recruited of which 53 were with autism and the remaining 37 were healthy controls. The ATP6 gene was amplified by PCR, purified, and sequenced by Sanger sequencing. In total forty-two genetic variants were identified within the gene. Among them 8886G > A and 8911 T > C were found to be associated with higher lactic acid levels and 8748C > T, 8886G > A, and 8964C > T were associated with higher ammonia levels after the adjustment with age, gender, and disease response. Additionally, all the synonymous variants were found to alter the relative synonymous codon usage (RSCU) values, potentially affecting the protein's structure and translation rate. Although there was no significant association between any ATP6 variants and disease outcomes, the variants associated with mitochondrial dysfunction as reflected by abnormal levels of lactic acid and ammonia may provide an improved understanding of the pathophysiology of ASD. Therefore they need to be explored further along with other components of the electron transport complex.

The Mitogenome of the Haecon-5 Strain of Haemonchus contortus and a Comparative Analysis of Its Nucleotide Variation with Other Laboratory Strains.

Haemonchus contortus (the barber's pole worm)-a highly pathogenic gastric nematode of ruminants-causes significant economic losses in the livestock industry worldwide. H. contortus has become a valuable model organism for both fundamental and applied research (e.g., drug and vaccine discovery) because of the availability of well-defined laboratory strains (e.g., MHco3(ISE).N1 in the UK and Haecon-5 in Australia) and genomic, transcriptomic and proteomic data sets. Many recent investigations have relied heavily on the use of the chromosome-contiguous genome of MHco3(ISE).N1 in the absence of a genome for Haecon-5. However, there has been no genetic comparison of these and other strains to date. Here, we assembled and characterised the mitochondrial genome (14.1 kb) of Haecon-5 and compared it with that of MHco3(ISE).N1 and two other strains (i.e., McMaster and NZ_Hco_NP) from Australasia. We detected 276 synonymous and 25 non-synonymous single nucleotide polymorphisms (SNPs) within Haecon-5. Between the Haecon-5 and MHco3(ISE).N1 strains, we recorded 345 SNPs, 31 of which were non-synonymous and linked to fixed amino acid differences in seven protein-coding genes (nad5, nad6, nad1, atp6, nad2, cytb and nad4) between these strains. Pronounced variation (344 and 435 SNPs) was seen between Haecon-5 and each of the other two strains from Australasia. The question remains as to what impact these mitogenomic mutations might have on the biology and physiology of H. contortus, which warrants exploration. The high degree of mitogenomic variability recorded here among these strains suggests that further work should be undertaken to assess the nature and extent of the nuclear genomic variation within H. contortus.

Mitochondrial Pathogenic Mutations and Expression Pattern of Oxidative Phosphorylation Genes in COVID-19 Patients

Mitochondrial missense mutations and pathogenic variants have been implicated in the pathogenesis of COVID‐19. This study evaluated the role of mitochondrial DNA (mtDNA) mutations and changes in gene expression in the progression of COVID-19 and their correlation with clinical characteristics. Next‐generation sequencing with high throughput was used to identify mtDNA mutations in 30 COVID-19 patients compared to 20 healthy controls. The potential impact of identified mutations on protein structure and stability was predicted using bioinformatic tools. Quantitative real-time polymerase chain reaction was employed to assess the expression levels of mtDNA-encoded genes involved in oxidative phosphorylation in COVID-19 patients and healthy controls. Correlations between gene expression levels, clinical parameters, including leukocyte, lymphocyte, neutrophil, and platelet count, as well as creatinine, alanine transaminase (ALT), aspartate transaminase (AST), and blood urea nitrogen (BUN) levels, and disease severity were analyzed. We found 8 different mtDNA mutations in ND1, ND5, CO3, ATP6, and CYB genes, which were predicted to alter amino acids and decrease protein stability. Two missense unique mutations, C9555T in CO3 and A12418T in ND5 were identified and correlated with Complexes I and IV, respectively. This downregulation was correlated with age, elevated levels of leukocytes, lymphocytes, neutrophils, platelets, creatinine, ALT, AST, and BUN, as well as disease severity. These findings suggest that mtDNA mutations and altered expression of oxidative phosphorylation genes contribute to mitochondrial dysfunction in COVID-19. Targeting mitochondrial dysfunction may represent a promising therapeutic strategy for COVID-19 treatment.

The Toxoplasma gondii homolog of ATPase inhibitory factor 1 is critical for mitochondrial cristae maintenance and stress response.

The production of energy in the form of ATP by the mitochondrial ATP synthase must be tightly controlled. One well-conserved form of regulation is mediated via ATPase inhibitory factor 1 (IF1), which governs ATP synthase activity and gene expression patterns through a cytoprotective process known as mitohormesis. In apicomplexans, the processes regulating ATP synthase activity are not fully elucidated. Using the model apicomplexan Toxoplasma gondii, we found that knockout and overexpression of TgIF1, the structural homolog of IF1, significantly affected gene expression. Additionally, TgIF1 overexpression resulted in the formation of a stable TgIF1 oligomer that increased the presence of higher order ATP synthase oligomers. We also show that parasites lacking TgIF1 exhibit reduced mitochondrial cristae density, and that while TgIF1 levels do not affect growth in conventional culture conditions, they are crucial for parasite survival under hypoxia. Interestingly, TgIF1 overexpression enhances recovery from oxidative stress, suggesting a mitohormetic function. In summary, while TgIF1 does not appear to play a role in metabolic regulation under conventional growth conditions, our work highlights its importance for adapting to stressors faced by T. gondii and other apicomplexans throughout their intricate life cycles.

Mitochondrial genome variants associated with amyotrophic lateral sclerosis and their haplogroup distribution.

Amyotrophic lateral sclerosis (ALS) may be familial or sporadic, and twin studies have revealed that even sporadic forms have a significant genetic component. Variants in 55 nuclear genes have been associated with ALS and although mitochondrial dysfunction is observed in ALS, variants in mitochondrial genomes (mitogenomes) have not yet been tested for association with ALS. The aim of this study was to determine whether mitogenome variants are associated with ALS. We conducted a genome-wide association study (GWAS) in mitogenomes of 1965 ALS patients and 2547 controls. We identified 51 mitogenome variants with p values <10-7, of which 13 had odds ratios (ORs) >1, in genes RNR1, ND1, CO1, CO3, ND5, ND6, and CYB, while 38 variants had OR <1 in genes RNR1, RNA2, ND1, ND2, CO2, ATP8, ATP6, CO3, ND3, ND4, ND5, ND6, and CYB. The frequencies of haplogroups H, U, and L, the most frequent in our ALS data set, were the same in different onset sites (bulbar, limb, spinal, and axial). Also, intra-haplogroup GWAS revealed unique ALS-associated variants in haplogroups L and U. Our study shows that mitogenome single nucleotide variants (SNVs) are associated with ALS and suggests that these SNVs could be included in routine genetic testing for ALS and that mitochondrial replacement therapy has the potential to serve as a basis for ALS treatment.

Assembly and comparative analysis of the complete mitochondrial genome of Fritillaria ussuriensis Maxim. (Liliales: Liliaceae), an endangered medicinal plant.

Fritillaria ussuriensis is an endangered medicinal plant known for its notable therapeutic properties. Unfortunately, its population has drastically declined due to the destruction of forest habitats. Thus, effectively protecting F. ussuriensis from extinction poses a significant challenge. A profound understanding of its genetic foundation is crucial. To date, research on the complete mitochondrial genome of F. ussuriensis has not yet been reported. The complete mitochondrial genome of F. ussuriensis was sequenced and assembled by integrating PacBio and Illumina sequencing technologies, revealing 13 circular chromosomes totaling 737,569 bp with an average GC content of 45.41%. A total of 55 genes were annotated in this mitogenome, including 2 rRNA genes, 12 tRNA genes, and 41 PCGs. The mitochondrial genome of F. ussuriensis contained 192 SSRs and 4,027 dispersed repeats. In the PCGs of F. ussuriensis mitogenome, 90.00% of the RSCU values exceeding 1 exhibited a preference for A-ended or U-ended codons. In addition, 505 RNA editing sites were predicted across these PCGs. Selective pressure analysis suggested negative selection on most PCGs to preserve mitochondrial functionality, as the notable exception of the gene nad3 showed positive selection. Comparison between the mitochondrial and chloroplast genomes of F. ussuriensis revealed 20 homologous fragments totaling 8,954 bp. Nucleotide diversity analysis revealed the variation among genes, and gene atp9 was the most notable. Despite the conservation of GC content, mitogenome sizes varied significantly among six closely related species, and colinear analysis confirmed the lack of conservation in their genomic structures. Phylogenetic analysis indicated a close relationship between F. ussuriensis and Lilium tsingtauense. In this study, we sequenced and annotated the mitogenome of F. ussuriensis and compared it with the mitogenomes of other closely related species. In addition to genomic features and evolutionary position, this study also provides valuable genomic resources to further understand and utilize this medicinal plant.

The complete mitochondrial genome of Mya japonica (Jay, 1857 Myida:myidae)

The soft-shell clam Mya japonica (Jay, 1857) is a commercially important fishery resource. In this study, we identified the complete mitochondrial genome of M. japonica and performed a phylogenetic analysis to explore its genetic relationship with Mya arenaria. The genome is 21,396 bp in length and contains 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 5 D-Loop control regions. The atp8 gene was annotated in Myidae for the first time. Notably, the genome contains an additional trnM, consistent with M. arenaria. The length of the cox2 gene is 1,947 bp, which is 513 bp longer than that in M. arenaria. Its base composition is 29.14% A, 37.26% T, 10.89% C, and 22.71% G. Phylogenetic analysis based on 12 PCGs and 2 rRNAs indicates that M. japonica and M. arenaria form a sister group. In this study, the identification and phylogenetic analysis of the complete mitochondrial genome of M. japonica provide significant information for future taxonomic and evolutionary research of the genus Mya.

Comparative genomic and phylogenetic analysis of the complete mitochondrial genome of Cricula trifenestrata (Helfer) among lepidopteran insects.

Cricula trifenestrata Helfer (commonly known as Amphutukoni muga/Cricula silkworm), a wild sericigenous insect produces golden yellow silk similar to Antheraea assamensis (muga silkworm), with significant potential as a natural fiber and biomaterial. Cricula is considered as a pest as it competes for food with muga, which produces the prized golden silk. This study focuses on decoding the mitochondrial genome of C. trifenestrata using next-generation sequencing technology and includes comparative analysis with Bombycoids and other lepidopteran insects. We found that the Cricula mitogenome spans 15 425bp and exhibits typical gene content and arrangement consistent with other Saturniids and lepidopterans. All protein-coding genes were found to undergo purifying selection, with the highest and lowest conservation observed in the cox1 and atp8 gene, respectively, indicating their potential role in future evolutionary events. We identified two types of mismatches: 23 "G-U" and 6 "U-U" pairs, similar to those found in Actias selene among the Saturniids. Additionally, our study uncovered the presence of two 33bp repeat units and a "TTAGA" motif in the control region, in contrast to the typical "ATAGA" motif, suggesting functional similarity with evolving sequences. Furthermore, phylogenetic analysis supports the close relationship of Cricula with other species within the Saturniidae family.

Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination

Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.

Assemble and comparative analysis of the mitochondrial genome of Rhododendron delavayi: Insights into phylogenetic relationships and genomic variations

Rhododendron delavayi, a notable ornamental plant primarily found in regions of China like Yunnan and Guizhou provinces, holds substantial horticultural value. To elucidate the systematic phylogenetic relationships and organelle genomic differences within R. delavayi and related Rhododendron species, we conducted sequencing and assembly of the complete mitochondrial genome of R. delavayi. The full-length mitochondrial genome of it was a singular circular molecule spanning 1,009,263 bp, comprising 53 protein-coding genes, including 18 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 32 protein-coding genes. A total of 1,182 simple sequence repeats (SSRs) loci were identified in the R. delavayi mitochondrial genome, primarily consisting of single nucleotide, dinucleotide, and trinucleotide repeats. Nucleotide diversity analysis highlighted five genes (atp6, atp9, cox2, nad1, and rpl10) with the highest diversity within the mitochondrial genomes of Rhododendron genus. Comparative analysis of the mitochondrial genome of R. delavayi with those of four other Rhododendron species indicated complex rearrangements in 21 genes, including rps4, nad6, rps3, atp6, cob, atp9, nad7, among others. The mitochondrial phylogenetic tree revealed a close relationship between R. delavayi and R. decorum, forming a sister clade to R. × pulchrum and R. simsii. Furthermore, 126 plastid-to-mitochondrial gene transfers in R. delavayi were identified, ranging from 30 bp to 19,385 bp. These fragments collectively constituted 47.54 % and 9.52 % of the chloroplast and mitochondrial genomes (202,169 bp), respectively. Complex mitochondrial-to-mitochondrial transfers were also observed, with 843 identified fragments totaling 312,036 bp (30.92 % of the mitochondrial genome). Segments exceeding 10 kb may mediate homologous recombination within the mitochondrial molecules. Remarkably, our study underscores that the mitochondrial genome of R. delavayi was the largest reported within the Rhododendron genus to date. The intricate rearrangements observed in the mitochondrial genomes of Rhododendron species, alone with the identification of five potential molecular marker sites, provided valuable insights for species classification and parentage identification within the Rhododendron genus.