Nad1 Gene Research Articles

Molecular characterization and genetic variability of Toxocara vitulorum from naturally infected buffalo calves for the first time in Bangladesh.

Toxocara vitulorum is one of the deadliest parasite of buffalo calves in Bangladesh. This study was conducted to explore genetic variability within and among the T. vitulorum populations in buffalo calves of Bangladesh. Genomic DNA was extracted, ITS2, COX1 and NAD1 gene were amplified and sequenced. Distinct 29 ITS2, 21 unique NAD1 and 24 COX1 genotypes were detected among the T. vitulorum of different geographic regions. These three gene genotypes similarities ranged from 97 to 99%, when these were compared to best hit scoring T. vitulorum sequences retrieved from GenBank. A total of 12 and 6 unique haplotypes were detected for COX1 and NAD1 gene sequences. The average nucleotide and haplotype diversity for COX1 and NAD1 were 0.0931 & 0.89493 and 0.00658 & 0.77895 respectively and the recorded values were more dispersed than previously published values. The pairwise Nst values ranged from −0.050 to 0.602 and Fst from −0.050 to 0.600 between all the T. vitulorum genotypes indicated huge genetic differentiation which were reportedly higher than other published reports Fst values. This is the first report of T. vitulorum on the basis of COX1 gene in Bangladesh. The study findings will be helpful for further extensive epidemiological studies regarding anthelmintic resistance, control and prevention of T. vitulorum infection in buffalo calves.

Synchronously improving intracellular electron transfer in electron-donating bacteria and electron-accepting methanogens for facilitating direct interspecies electron transfer during anaerobic digestion of kitchen wastes

Two major issues generally limit the effectiveness of direct interspecies electron transfer (DIET) during anaerobic digestion: 1) lack of essential electrical connection component, electrically conductive pili (e-pili) or multi-heme c-type cytochrome (MHC); 2) the thermodynamic limitations of combining electrons with protons for reducing carbon dioxide to methane. To address both issues, a strategy for facilitating DIET via combining ethanol-type fermentation pretreatment (EFP) with NaCl addition during anaerobic digestion of kitchen wastes was proposed. Combining EFP with NaCl addition dramatically increased methane yield rates (531.3 ± 11.4 vs 410.5 ± 8.7 mL/gVSadded/d) and efficiencies of conversion of organic substrates to methane (571.2 ± 13.8 vs 488.7 ± 11.7 mL/gVSremoval). The increased performances by combining EFP with NaCl addition were higher than that by independent EFP or NaCl addition. Paludibacter sp., Petrimonas sp. and Syntrophomonas wolfei were the predominant and metabolically active electron-donating bacteria, and their expression of genes for e-pili/MHCs by combining EFP with NaCl addition was higher than that by independent EFP or NaCl addition. Methanothrix soehngenii and Methanoculleus bourgensis were the predominant and metabolically active electron-accepting methanogens, and their expression of genes for carbon dioxide reduction pathway for methanogenesis by combining EFP with NaCl addition was higher than that by independent EFP or NaCl addition. In addition, EFP specifically increased the transcript abundance of genes for NAD+/NADH transformation closely associated with the formation of e-pili/MHCs, while NaCl addition specifically increased the transcript abundance of genes for coenzyme F420/F420H2 transformation known to participate in reduction of carbon dioxide to methane.

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.

First molecular characterisation of Hydatigera taeniaeformis (Cestoda: Taeniidae) from Rattus rattus in urban market centres from Tamale, Ghana

BackgroundThe common cat tapeworm, Hydatigera taeniaeformis, is widely distributed across many regions of the world but its global genetic diversity, ecology, and other biological features are not fully understood. The predator-prey relationship of felids and rodents sustains the transmission in both sylvatic and synanthropic or urban settings. This study was carried out in three urban market centres in Tamale, Ghana to determine the prevalence of H. taeniaeformis infection in urban rats and characterise the local population genetics using the mitochondrial nad1 gene sequences.MethodsFrom January to May 2023, rats were captured and euthanized to identity and isolate the H. taeniaeformis metacestodes. The full mitochondrial nad1 gene was amplified, sequenced and used to characterise the cestode population.ResultsIn total 64/80 rats from the three market centres were found naturally infected with metacestodes of H. taeniaeformis. Averagely, infected rats harboured two cysts with one exceptional case of 25 cysts in one liver. Each cyst harboured one metacestode. The DNA sequences revealed four haplotypes in a star-like distribution network across the three market centres. All four haplotypes were found to be unique, clustered with H. taeniaeformis sensu stricto (s.s.) global isolates and had only marginal variation among themselves.ConclusionThis is the first account of the genetic variability within H. taeniaeformis in Ghana and would contribute to ongoing and future studies on African regional biogeographic distribution of the common cat tapeworm.

Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives

BackgroundTerniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported.ResultsIn current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes.ConclusionsThis study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.

Mangiferin activates the nuclear factor erythroid 2-related factor pathway to protect SOD1-G93A induced NSC-34 motor neurons from oxidative stress and apoptosis.

One of the main factors in the pathophysiology of amyotrophic lateral sclerosis is oxidative stress. Mangiferin (MF), a natural plant polyphenol, has anti-inflammatory and antioxidant effects. The aim of our study was to investigate the protective effects and mechanisms of MF in the hSOD1-G93A ALS cell model. Our result revealed that MF treatment reduced the generation of reactive oxygen species (ROS) and malondialdehyde (MDA), decreased oxidative damage, and reduced apoptosis. Additionally, it was observed that MF significantly increased the synthesis of the antioxidant genes hemeoxygenase-1 and NAD(P)H: quinone oxidoreductase 1, which are downstream of the Nrf2 signaling pathway, and increased the expression and activation of nuclear factor erythroid 2-related factor 2 (Nrf2). Nrf2 knockdown greatly promoted apoptosis, which was reversed by MF treatment. To summarize, MF promoted the Nrf2 pathway and scavenged MDA and ROS to protect the ALS cell model.

Mitochondrial genome study of Camellia oleifera revealed the tandem conserved gene cluster of nad5-nads in evolution.

Camellia oleifera is a kind of high-quality oil supply species. Its seeds contain rich unsaturated fatty acids and antioxidant active ingredients, which is a kind of high-quality edible oil. In this study, we used bioinformatics methods to decipher a hexaploid Camellia oil tree's mitochondrial (mt) genome based on second-generation sequencing data. A 709,596 bp circular map of C. oleifera mt genome was found for the first time. And 74 genes were annotated in the whole genome. Mt genomes of C. oleifera and three Theaceae species had regions with high similarity, including gene composition and gene sequence. At the same time, five conserved gene pairs were found in 20 species. In all of the mt genomes, most of nad genes existed in tandem pairs. In addition, the species classification result, which, according to the gene differences in tandem with nad5 genes, was consistent with the phylogenetic tree. These initial results provide a valuable basis for the further researches of Camellia oleifera and a reference for the systematic evolution of plant mt genomes.

New species of Kontrimavichusia Makarikov & Binkienė, 2022 (Eucestoda: Hymenolepididae) from arvicoline rodents (Rodentia: Cricetidae) from the North Caucasus

Two previously unrecognized species attributable to the genus Kontrimavichusia Makarikov & Binkienė, 2022 in arvicoline rodents from the North Caucasus are described. Kontrimavichusia testiculata sp. nov. is described from Microtus majori (Thomas, 1906) from the northwestern Caucasus (Republic of Adygeya and Karachay-Cherkess Republic, Russia) and Kontrimavichusia hobergi sp. nov. is described from Microtus daghestanicus (Shidlovsky, 1919) from the central Caucasus (Republic of North Ossetia, Russia). Kontrimavichusia testiculata is readily distinguishable from K. asymmetrica (Janicki, 1904) and K. hobergi in having a larger number of testes (4–6 per proglottis), larger suckers and a longer cirrus and cirrus-sac. In addition, the new species differs from its congeners by the position of the cirrus-sac with regard to the poral osmoregulatory canals and position of distal end of the rostellar pouch relative to the posterior margins of the suckers. Kontrimavichusia hobergi can be readily distinguished from its congeners by the arrangement of the testes in a triangle and the position of the cirrus-sac with regard to the poral osmoregulatory canals. In addition, this previously unrecognized species differs from K. asymmetrica and K. testiculata by the smaller dimensions of the fully developed strobila and a narrower ovary. The cirrus-sac of K. hobergi is larger than that in K. asymmetrica but smaller than that in K. testiculata. We also used partial sequences of the nuclear ribosomal 28S rRNA gene and mitochondrial nad1 gen to justify the generic arrangement and independent status of these two new species which are characterized in the current manuscript.

Molecular identification and genetic variability of equine and bovine ocular setariasis in india: molecular profiling by mitochondrial genes.

Ocular setariasis is an ectopic infection caused by a parasite under the genus Setaria. Adult worms belong to the Setariidae family and typically reside in the peritoneal cavity of ungulates. However, immature forms of these species may aberrantly migrate to the eyes of cattle, buffalo, goats, horses and several other hosts, leading to corneal opacity and blindness. Here, we have distinguished the Setaria digitata collected from both equine and buffalo hosts based on the morphology, molecular profiling of mitochondrial cytochrome c oxidase subunit 1 (Cox1), cytochrome c oxidase subunit 3 (Cox3) and, Nicotinamide Adenine Dinucleotide dehydrogenase subunit 1 (NAD1) genes. A single filarial worm was collected from the eye of one equine and one bovine host. These worms were then processed for morphological examination and DNA isolation. Cox1, Cox3 and NAD1 genes were amplified using specific primers and subjected to custom sequencing. The sequences were then used for multiple sequence alignment, assessment of entropy, similarity and haplotype diversity analysis. Key morphological features confirmed the worms collected were male and female Setaria digitata from equine and buffalo hosts, respectively. Cox1, Cox3 and NAD1 gene sequence analysis showed a close association of S.digitata Indian isolates with its counterparts from Sri Lanka and China isolates. The phylogram of bovine S. digitata sequences shows a close relationship to other equine S. digitata sequences, indicating the need for further in-depth studies on the prevalence of infection across various host species and intermediate hosts. Although the sequence results suggest that S. digitata is likely the causative agent of ocular setariasis in India, additional samples are needed to confirm this conclusion. Comprehensive analysis of the transcriptome and proteome of S. digitata from both bovine and equine hosts is necessary to explore variations in host-parasite interactions. These findings will aid in future parasite identification, investigations into vector prevalence in India, and the development of control measures against ocular setariasis.

Study of the population genetic structure of Opisthorchis-like eggs in northern Thailand using mitochondrial genes.

Opisthorchis-like eggs are a public health problem in northern and northeastern Thailand. However, the genetic epidemiology and structure of these parasites in northern Thailand are unknown. Thus, this study investigated their population genetic structure using cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) nucleotide sequences. A study was conducted in the hill tribe regions of Chiang Mai Province, northern Thailand. Internal transcribed spacer 2 polymerase chain reaction and restriction fragment length polymorphism were used to distinguish 205 positive feces samples for Opisthorchis-like eggs. The results showed that the prevalence of O. viverrini and Haplorchis taichui was 10.5% and 38.2%, respectively, and the co-infection rate was 37.2%. To determine the genetic structure of O. viverrini and H. taichui using cox1 and nad1 genes, genetic analysis was performed using 30 randomly chosen fecal samples for Opisthorchis-like eggs. Pairwise FST analysis indicated that O. viverrini and H. taichui displayed nonsignificant genetic differentiation within Chiang Mai Province and between interpopulations from different geographic areas. Moreover, within the intrapopulation in Chiang Mai Province,cox1 presented higher gene flow than nad1 in O. viverrini, while nad1 demonstrated higher gene flow than cox1 in H. taichui. The neutrality tests based on Fu's Fs indicated population expansion and selective sweep from bottleneck or hitchhiking in O. viverrini and H. taichui populations, supported by haplotype network patterns. Phylogenetic tree analysis based on cox1 and nad1 revealed the monophyly of O. viverrini and H. taichui and genetic relationships with other isolates collected from Thailand, Lao People's Democratic Republic (PDR), and Vietnam. This study investigated the molecular discrimination and genetic structure of Opisthorchis-like eggs in northern Thailand. The genetic information derived from this study could be associated with the background, molecular epidemiology, and disease severity of these parasites.

Environmental contamination with feces of free-roaming dogs and the risk of transmission of Echinococcus and Taenia species in urban regions of southeastern Iran

BackgroundDogs are the most important definitive hosts of zoonotic taeniid helminths worldwide. Different Echinococcus and Taenia species of domestic and wild carnivores pose a potential risk to human population. High populations of free-roaming dogs (FRDs) in urban areas of Iran and widespread contamination of the environment with dog feces is a potential source of infecting people living in the urban regions with cystic echinococcosis (CE). Our knowledge on the risk of CE transmission in the urban settings in the endemic regions is limited. The present study surveyed the species and genotypes of E. granulosus sensu lato and other taeniids by examining feces of free-roaming dogs in the urban areas in the city of Kerman, southeastern Iran.MethodsThe city was divided into 100 consecutive blocks of which 25 blocks were randomly selected. Fecal samples of FRDs were counted, mapped and fresh samples were collected. Then Zinc chloride flotation, and sequential sieving was performed, and the samples were examined under an inverted microscope. Single individual taeniid eggs were isolated, partial nad1 gene was amplified and sequenced to identify species and genotypes.ResultsIn total 5607 fecal samples of dogs were mapped and 83 fresh samples were collected. Taeniid eggs were detected in nine fecal samples (10.8%) from seven out of the 25 city blocks (28.0%). Echinococcus eggs were found in four samples (4.8%) from three city blocks, two samples containing E. granulosus sensu stricto (2.4%), two samples containing E. canadensis G6/7 (2.4%). In addition, three samples contained eggs of Taenia hydatigena (3.6%), and one sample of Taenia serialis (1.2%).ConclusionsThis study documented the potential risk of CE transmission to humans resulting from the feces of dogs roaming freely in urban areas.Graphical

Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.

Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.

Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics.

Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.

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.

Effects of intradialytic bicycle ergometer exercise on transcription factors NF-ĸB and Nrf2 in patients with chronic kidney disease: A randomized crossover clinical trial

PurposeTo evaluate the effects of an intradialytic aerobic exercise training program on the expression of transcription factors nuclear factor κappa B (NF-κB) and nuclear factor erythroid 2-related factor 2 (Nrf2), related to inflammatory and antioxidant pathways, respectively, in patients with chronic kidney disease (CKD) on hemodialysis. MethodsThis was a longitudinal, randomized clinical trial with a washout period and crossover performed with 33 patients randomized into two groups: Exercise (individualized intradialytic aerobic exercise on an adapted stationary exercise bike) three times per week for three months and control (without exercise). After the washout period (1 month), the exercise group became the control, and the other group performed the exercises for another three months. Blood sample collection, food intake, and anthropometry were evaluated at the beginning and end of each study phase. Nrf2, its target gene NAD(P)H quinone oxidoreductase 1 (NQO1), and NF-κB transcription factors were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) and the inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) by ELISA assay. ResultsEighteen patients [11 men, 44.1 ± 8.4 years, 17.3 (6.6–124) months on HD] completed all the study. The obtained data revealed that the intervention did not affect Nrf2, NQO1, and NF-κB mRNA expression. Also, TNF-α levels were not changed. However, IL-6 showed a tendency to decrease after the exercise intervention (p = 0.054). ConclusionIn hemodialysis patients, three months of intradialytic aerobic exercise did not modulate the transcription factors associated with inflammation (NF-κB) and antioxidant activity (Nrf2 and NQO1). Clinical trials registration numberNCT04375553.

Characterizing the complete mitogenome of Odontothrips phaseoli (Thysanoptera: Thripidae) and its mitochondrial phylogeny

Described originally from Heilongjiang, China, Odontothrips phaseoli is a potential pest of threatening bean plant in northern China. The complete mitochondrial genome of O. phaseoli was sequenced and assembled, with a total length of 15,540 bp. Within this genome, 37 genes have been identified: 13 PCGs, 22 tRNAs, two rRNAs, and two putative control regions. Most PCGs terminate with TAA, while four genes (atp8, nad1, nad2 and nad4) use an incomplete ‘T’ and nad6 employs TAG as the stop codon. Compared to the mitogenome of the ancestral insect, O. phaseoli displays significant gene rearrangement. However, it retains three conserved gene blocks in common with its related species, Megalurothrips usitatus, both of which belong to the Megalurothrips genus-group. The phylogenetic tree, constructed based on the entire mitogenome dataset of all thrips species available in NCBI, shows that the two species cluster closely together. This alignment might underscore the close link between gene arrangements and the phylogeny relationships.

Effect of storage temperature on viral RNA accumulation in Plum pox virus-infected Red Lyon plum fruit from the Central Valley of Chile

Plum pox virus (PPV), the causative agent of Sharka disease, causes serious economic losses to the stone fruit industry. As PPV is not transmitted by seed, fruit from countries with Sharka present are considered low-risk for spreading the disease. However, there have been cases raising concerns about the safety of exporting fruit from countries with Sharka disease. Due to this, the generation of new scientific evidence becomes important to address these concerns. This study aimed to compare the relative accumulation of PPV viral titer between freshly harvested infected fruit with fruit subjected to cold storage, simulating transit conditions to export markets. During two consecutive seasons, the fruit was collected from a PPV-infected ’Red Lyon’ plum orchard, and divided into three treatments (T): freshly harvested fruit (T1); fruit exposed to cold (0 °C) for seven days (T2), and fruit exposed to cold (0 °C) for 15 days (T3). Semi-quantitative RT-PCR was used to estimate the viral titer; band density values obtained for products of amplification of a PPV genome fragment were normalized with the density values obtained from the constitutive gene nad5 and plotted relative to treatment T1, which served as a control for this purpose. The results showed a significant difference (p < 0.05) between T1 and other treatments. For the first season, the viral RNA reduction was of 50% in T2 and 61% in T3, compared to T1. For the second season, the corresponding RNA viral reductions were 45% in T2 and 56% in T3, compared to T1.

Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species.

Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.

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.

Phylogeography, Genetic Diversity and Population Structure of Echinococcus granulosus Sensu Stricto Inferred by Mitochondrial DNA Markers between Southeast of Iran and Pakistan.

Current study was designed to provide a better insight into the circulating genotypes, genetic diversity, and population structure of Echinococcus spp. between southeast of Iran and Pakistan. From Jun 2020 to Dec 2020, 46 hydatid cysts were taken from human (n: 6), camel (n: 10), goat (n: 10), cattle (n: 10) and sheep (n: 10) in various cities of Sistan and Baluchestan Province of Iran, located at the neighborhood of Pakistan. DNA samples were extracted, amplified, and subjected to sequence analysis of cox1 and nad1 genes. The phylogeny inferred by the Maximum Likelihood algorithm indicated that G1 genotype (n: 19), G3 genotype (n: 14) and G6 genotype (n: 13) assigned into their specific clades. The diversity indices showed a moderate (nad1: Hd: 0.485) to high haplotype diversity (cox1: Hd: 0.867) of E. granulosus s.s. (G1/G3) and low nucleotide diversity. The negative value of Tajima's D and Fu's Fs test displayed deviation from neutrality indicating a recent population expansion. A parsimonious network of the haplotypes of cox1 displayed star-like features in the overall population containing IR9/PAK1/G1, IR2/PAK2/G3 and IR18/G6 as the most common haplotypes. A pairwise fixation index (Fst) indicated that E. granulosus s.s. populations are genetically moderate differentiated between southeast of Iran and Pakistan. The extension of haplotypes PAK18/G1 (sheep) and PAK26/G1 (cattle) toward Iranian haplogroup revealed that there is dawn of Echinococcus flow due to a transfer of alleles between mentioned populations through transport of livestock or their domestication. The current findings strengthen our knowledge concerning the evolutionary paradigms of E. granulosus in southeastern borders of Iran and is effective in controlling of hydatidosis.