mtDNA Regions Research Articles

First Report of Meloidogyne enterolobii Infecting Yellow pitaya (Selenicereus megalanthus) in China.

Yellow pitaya, Selenicereus megalanthus, is a night-blooming, climbing cacti of tropical origin, which has received increasing attention for its potential as a new exotic fruit crop (Lichtenzveig et al. 2000). The crop is grown extensively in Hainan Province, China (3000 ha). In October 2021, a survey was conducted on a farm located in Changjiang (19°21'4″N, 108°47'2″S), Hainan Province, China. Some yellow pitaya plants were found that were stunted and chlorotic, with abnormally thin stems (Fig. 1B), and no symptoms on healthy plants (Fig. 1A). Dead plants were also observed. Many galls and females with egg masses were observed on roots (Figs. 1C & 1D). This is typical of root-knot nematode (RKN) infections, and the incidence of infection was 36.7%. Meloidogyne sp. females and egg masses were dissected from roots of the infected plants. The perineal pattern of females (n= 5) was round to oval-shaped with a high dorsal arch (Figs. 1I & 1J). Second-stage juveniles (J2s) had truncated lips (Figs. 1E & 1F) and long-conical tails with bluntly rounded tips (Figs. 1G & 1H). The J2s body length (n= 24) averaged 416.79 μm (349.21 to 472.76 μm) with a mean width of 15.36 μm (12.47 to 17.52 μm); mean stylet length was 11.16 μm (10.10 to 13.23 μm); tail length averaged 53.73 μm (43.46 to 65.90 μm). The morphological characteristics matched the original description of M. enterolobii (Yang and Eisenback 1983). Males were not found. Genomic DNA was extracted from eight single J2s, and the mitochondrial (mtDNA) region between COII and 16S rRNA gene was amplified with primers C2F3/1108 (Powers and Harris 1993). A 652-bp DNA fragment was obtained, for which the sequence (GenBank accession no. OP122499) was 100% identical to the sequences of M. enterolobii isolates from China（MN269947）and the USA (MN809527). Furthermore, species identification was also confirmed using M. enterolobii specific primers Me-F/Me-R. An amplicon size of ∼230 bp was obtained, which is consistent with those previously reported for M. enterolobii (Fig. 2) (Long et al. 2006). Therefore, this population was identified as M. enterolobii based on morphological and molecular characteristics. Pathogenicity tests were performed in the greenhouse at 26℃ and 80% relative humidity with a 14-h/10-h light/dark photoperiod. Ten RKN-free S. megalanthus seedlings were transplanted into pots containing sterilized soil. After 3 weeks, the roots of 5 plants were inoculated with 3,000 eggs and J2s of M. enterolobii per plant. Five uninoculated plants were used as control plants. After 2 months, no galling or symptoms were observed on the control plants. All inoculated plants had galled roots similar to those observed in the field. Females and egg masses were obtained by dissecting galls. The nematode reproduction factor (RF= final population/initial population) was 1.9. Adult females (n= 5) dissected from inoculated plants were identified as M. enterolobii with sequence-specific primers Me-F/Me-R, thus confirming pathogenicity. The pathogenicity test was carried out twice with similar results. M. enterolobii is one of the most damaging species of RKN, due to its wide host range, high level of pathogenicity, and ability to develop and reproduce on several crops with resistance genes to other RKN (Castagnone-Sereno 2012). To our knowledge, this is the first report of S. megalanthus (yellow pitaya) as a host of M. enterolobii in China. Further studies are needed to develop and evaluate integrated management strategies.

Morphological and molecular characterizations of Pratylenchus coffeae infecting Ming aralia and coffee in Vietnam.

Pratylenchus coffeae, belonging to the root-lesion nematode group, is a highly prevalent and destructive plant-parasitic nematode that is able to infest a wide range of host plants. Although this species' devastating impacts on coffee plantations across the world are widely known on other host plants, its association with Ming aralia has never been reported. Our study characterized two popu lations of P. coffeae (associated with Ming aralia and coffee) and compared them with other popu lations from previous studies in Vietnam and other countries in the world. The identification of P. coffeae in our study was confirmed by the comprehensive analysis encompassing morphological examination, morphometric data, and molecular characterizations of the COI mtDNA and D2D3 of 28S rRNA regions. The cluster and MDS analyses revealed that the two populations of P. coffeae from Vietnam are closely related to those from Japan and Indonesia. The D2-D3 sequences of 28S rRNA and COI mtDNA regions exhibited high similarity among these populations, indicating a stable genetic profile. Our research contributes to a better understanding of the distribution and genetic characterizations of P. coffeae by offering new morphological and molecular insights into the presence of this nematode in Vietnam. Additionally, this nematode species was found to be associated with host plant's symptoms such as chlorotic leaves, stunted growth and root lesion in both hosts. Given the economic significance of both Ming aralia and coffee crops in Vietnam, as well as the damaging potential of P. coffeae, this study emphasizes the need of proactive nematode management measures to control this destructive pest.

Barcoding and mitochondrial phylogenetics of Porites corals.

Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.

Genetic Structure of Gallus varius Based on Middle-Lower Section of Control Region mtDNA

Gallus varius, an indigenous bird species of Indonesia, demonstrates significant genetic diversity. The genetic diversity assessment in G. varius encompassed both mitochondrial DNA (mtDNA) and nuclear DNA, with the mtDNA analysis primarily centered on domain I of the control region. This study aimed to describe the genetic diversity and structure of G. varius inhabiting Java, Madura, Lombok and Sumbawa based on the middle-lower part of control region mtDNA. Genomic DNA was extracted from the calamus tip of feather, then the middle-lower part of control region was amplified and sequenced using two pairs of primers. In the examined control region, spanning from 944 to 1,008 bp, 13 bp of nucleotide variation was observed, with nucleotide diversity at 0.0021. Between G. varius samples and the reference (NC_007238.1), a total of 7 haplotypes were identified, 5 unique and 2 shared haplotypes, with haplotype diversity at 0.7692. The substantial diversity of haplotypes in this study and two previous study suggests that the genetic diversity of G. varius has remained stable over the past two decades. Additionally, genetic distance data indicate there is multiple G. varius subspecies, and the haplotype network accentuates signs of population differentiation.

Molecular characterization of the camel nasal botfly, Cephalopina titillator (Diptera: Oestridae)

BackgroundLarval stages of the camel nasal botfly, Cephalopina titillator (Diptera: Oestridae), rank among the top obligate endoparasites causing nasopharyngeal myiasis. Such infestations have adverse effects on camel health, reducing their economic value. The current study’s objective is to assess the applicability of PCR using partial regions of the COI mtDNA and 28S rRNA gene sequences to identify, classify, and reveal the phylogenesis of C. titillator.ResultsLarvae of the 2nd and 3rd instars of C. titillator were collected from the El-Bassatin abattoir in Egypt, extracted from the nasopharyngeal passage of the Arabian camel (Camelus dromedarius) during postmortem inspection. Genomic DNA was successfully isolated from 10 samples of 3rd instar larvae of C. titillator and amplified using primer pairs targeting partial mitochondrial COI (916 bp) and ribosomal 28S rRNA (830 bp) gene fragments. Nucleotide sequences from five samples have been sequenced and submitted to GenBank under accession numbers OP482168 to OP482172 for the COI gene and OP482160 to OP482164 for the 28S rRNA gene fragments. The COI gene exhibited 97.3% nucleotide identity across all specimens, while the 28S rRNA gene displayed 99.74% identical nucleotides. Maximum likelihood trees were constructed based on the generalized time-reversible (GTR) model. The resulting COI phylogenetic tree demonstrated that the subfamily Oestrinae does not exhibit monophyly. Additionally, it revealed that C. titillator is a sister group to the subfamily Gasterophilinae. Despite the scarcity of data available for the 28S rRNA gene, the phylogenetic analysis utilizing 28S rRNA revealed one distinct lineage for the Egyptian camel nasal bot fly.ConclusionsMolecular phylogenetic analysis was conducted using molecular markers of distinct origins (both mitochondrial and nuclear) to elucidate the evolutionary relationships within the family Oestridae. This analysis is particularly significant following the inclusion of C. titillator, a first-time discovery in Egypt.

RDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male)

BackgroundHybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood.ResultsThe observations showed that the hybrid grouper was diploid (2n = 48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis.ConclusionResults of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.

Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events

BackgroundThe aim of this study was to evaluate and characterize the mutations induced by two TALE-based approaches, double-strand break (DSB) induction by the FokI nuclease (mitoTALEN) and targeted base editing by the DddA cytidine deaminase (mitoTALECD), to edit, for the first time, the mitochondrial genome of potato, a vegetatively propagated crop. The two methods were used to knock out the same mitochondrial target sequence (orf125).ResultsTargeted chondriome deletions of different sizes (236–1066 bp) were induced by mitoTALEN due to DSB repair through ectopic homologous recombination of short direct repeats (11–12 bp) present in the target region. Furthermore, in one case, the induced DSB and subsequent repair resulted in the amplification of an already present substoichiometric molecule showing a 4288 bp deletion spanning the target sequence. With the mitoTALECD approach, both nonsense and missense mutations could be induced by base substitution. The deletions and single nucleotide mutations were either homoplasmic or heteroplasmic. The former were stably inherited in vegetative offspring.ConclusionsBoth editing approaches allowed us to obtain plants with precisely modified mitochondrial genomes at high frequency. The use of the same plant genotype and mtDNA region allowed us to compare the two methods for efficiency, accuracy, type of modifications induced and stability after vegetative propagation.

An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.

Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.

Genetic structure and diversity of green turtle (Chelonia mydas) in the Gulf of Thailand.

The International Union for the Conservation of Nature and Natural Resources lists the green turtle as endangered. Green turtle nesting behavior in the Gulf of Thailand has decreased to <50% of the 1995 level. The population structure of green turtles in the Gulf of Thailand has not yet been studied. This study aimed to characterize the genetic diversity of green turtles in the Gulf of Thailand based on comparisons of mitochondrial DNA (mtDNA) control region with sequences of Indo-Pacific management units (MUs) and rookeries, to investigate population structures, and to explore phylogeographic relationships. Blood samples (1 mL each) from 91 stranded green turtles were collected from four parts of the Gulf of Thailand (eastern, upper, central, and lower). The control mtDNA region was amplified by polymerase chain reaction using LCM15382 and H950 primer. The obtained 384-bp or 770-bp sequences were analyzed for haplotype, clade, and haplotype and nucleotide diversities and were used to construct a phylogenetic tree and haplotype network diagram, respectively. In addition, we analyzed genetic differentiation within and among populations of green turtles in the Gulf of Thailand and between green turtles in the Gulf of Thailand and other Indo-Pacific MUs and rookeries. In total, 12 (based on 384 bp) or 13 (based on 770 bp) haplotypes and two clades (clades VII and VIII) were identified, with nine or 10 haplotypes belonging to clade VIII and three haplotypes belonging to clade VII. Of the new haplotypes, four or five were identified and classified as clade VII (two haplotypes, for both fragment lengths) and clade VIII (two or three haplotypes, for 384 bp or 770 bp fragments, respectively). The overall haplotype and nucleotide diversity of green turtles in the Gulf of Thailand were high (0.755 ± 0.039 and 0.01146 ± 0.00248, respectively). Based on the analysis of molecular variance, green turtles in the Gulf of Thailand could be divided into two subpopulations (UC-Eastern Gulf of Thailand [UC-EGT] and lower Gulf of Thailand [LGT]). Comparisons with other MUs and rookeries in the Indo-Pacific showed that UC-EGT was not genetically different from the Peninsular Malaysia and Eastern Taiwan (Lanyu) MUs and the Terrangganu and Mersing rookeries, and LGT were not genetically different from Peninsular Malaysia, Sipadan, Brunei Bay, Eastern Taiwan (Lanyu), Scott Reef and Browse Island, and Gulf of Carpentaria MUs and the Perak, Perhentain Island, Redang, Pahang, and Vietnam rookeries. To the best of our knowledge, this is the first report to identify the haplotypes and clades of green turtles in the Gulf of Thailand and to show that the populations in the Gulf of Thailand not only present high genetic diversity but also have haplotypic endemism. Longer mtDNA fragments (770 bp) increased the resolution of the stock structure. Clade VII is a unique clade not only for Japan but also for Thailand and Malaysia, and CmP82 is a unique haplotype for both the Gulf of Thailand and Malaysia. Conservation and management of these populations are important to preserve the genetic diversity, biological diversity, and evolutionary potential of green turtles in the Gulf of Thailand.

Taxonomy and phylogeny of three rust fungi parasitic on Vitaceae in Korea, with Neophysopella viticola sp. nov. on Vitis vinifera

Rust fungi are important pathogens of trees, ornamental plants, and food crops. Field research targeting rust diseases across Korea uncovered three distinct species of Neophysopella,affecting different members of the family Vitaceae. In our examination of both wild and cultivated grapevine (Vitis) species, including V. amurensis, V. coignetiae, and V. vinifera, we found N. meliosmaemyrianthae as well as a previously undescribed rust species, which we describe here as N. viticola sp.nov. Neophysopella ampelopsidis, which was previously identified as a rust pathogen of Vitis spp., has been observed to specifically infect Ampelopsis brevipedunculata. Through molecular sequenceanalysis of the ITS, LSU rDNA, and cox3 mtDNA regions, we determined the phylogenetic placements of these three species. Our morphological studies revealed the distinguishing features of N. viticola, particularly its unique teliospore layer and urediniospore dimensions. The emergence of N. viticola oneconomically valuable grapevines raises concerns about potential agricultural losses, highlighting the urgency for developing specialized management approaches in viticulture.

Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals.

The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.

Novel haplotypes of the COI-COII mtDNA region in the dark forest bee, Apis mellifera mellifera L., 1758

Novel haplotypes of the COI-COII mtDNA region in the dark forest bee, Apis mellifera mellifera L., 1758

Report of Phytophthora capsici (mating type A1) isolates associated with crown‐rot disease of Capsicum annuum in Guatemala

AbstractWilting and crown‐rot symptoms were observed in sweet pepper (Capsicum annuum) plants in field surveys carried out in 2021 across major vegetable‐producing areas of three municipalities of Guatemala. Phytophthora capsici (Peronosporales, Peronosporaceae) isolates were identified in association with these symptoms based upon morphological and phylogenetic analyses using nucleotide sequence information of the Cox2 mitochondrial DNA (mtDNA) region. Biological tests confirmed P. capsici mating type A1 isolates as the causal agents of the disease. Symptoms similar to those observed in the field were obtained after controlled inoculation of C. annuum ‘Tico’ seedlings. Solanum habrochaites ‘LA 404’ and C. annuum ‘Criollo de Morelos’ displayed strong resistance reaction against all Guatemalan isolates. Even though P. capsici is a cosmopolitan pathogen, this is the first molecular confirmation of this pathogen infecting C. annuum in Guatemala.

Assesment of Hypoderma infestation in a wild population of Cervus elaphus from mountains Atlantic ecosystems in southwestern Europe (Spain)

Hypodermosis in Cervus elaphus was studied in the Riaño Regional Hunting Reserve, Province of León, north-western Spain. One hundred and ten red deer were examined for the presence of warble fly larvae. They were analyzed by PCR analysis of the COI region of mt-DNA and identified as Hypoderma actaeon. The prevalence of larvae was 42.7% with a mean intensity of 12.5 ± 18 (range 1–80) warbles/deer infested. The distribution of larvae in the infested animals showed an aggregated/overdispersed pattern (aggregation index = 25.84), where the larvae are not randomly or uniformly distributed, but strongly aggregated among their hosts. Larvae were found in all three states. First and second-instars were observed mainly in the autumn until the end of winter (November-March) and third-instars in late winter until mid-spring (March–May). The adult animals and the males had a higher prevalence than the young and the females, finding statistically significant differences only according to the sex of the animals. Seasonal variations were observed in the prevalence with the highest number of infested animals in winter and autumn, but not in terms of the mean intensity of parasites. Additionally, we assessed the presence of anti-Hypoderma antibodies in serum by means of indirect ELISA tests, using a crude larval extract (CLE) and a purified fraction the hypodermin C (HyC) obtained from first instars of Spanish isolates of Hypoderma lineatum (cattle). These findings confirm that H. actaeon is widely distributed in northern Spain, and provide new information about its chronobiology in mountainous Atlantic ecosystems from southwestern Europe.

Trends of Eurasian Perch (Perca fluviatilis) mtDNA ATP6 Region Genetic Diversity within the Hydro-Systems of the Eastern Part of the Baltic Sea in the Anthropocene.

The intraspecific genetic diversity of freshwater fish inhabiting hydro-systems of the macrogeographic area spreading from the Black to Baltic Seas requires comprehensive investigation from fundamental and practical perspectives. The current study focused on the involvement of the mtDNA ATP6 region in the adaptability and microevolution of Perca fluviatilis within phylogeographic and anthropogenic contexts. We sequenced a 627 bp fragment encompassing the ATP6 region and used it for genetic analysis of 193 perch caught in Latvia, Lithuania, Belarus, and Ukraine, representing natural and anthropogenically impacted populations. We evaluated patterns of intraspecific genetic diversity in the ATP6 region and phylogeographic trends within the studied area compared with previously established D-loop trends. Evaluation of ATP6 coding sequence variability revealed that among 13 newly detected haplotypes, only two were caused by non-synonymous substitutions of amino acids of the protein. PCoA revealed three genetic groups (I-III) based on the ATP6 region that encompassed four previously described genetic groups established based on the mtDNA D-loop. The two mtDNA regions (D-loop and ATP6) have microevolved at least partially independently. Prolonged anthropogenic impacts may generate new point mutations at the ATP6 locus, but this phenomenon could be mainly concealed by natural selection and reparation processes.

First report of Meloidogyne javanica infecting Bletilla striata in Yunnan, China.

Bletilla striata (Thunb. ex Murray) Rchb. F. (Orchidaceae) is an endangered traditional Chinese medicinal plant and has been traditionally used for hemostasis and detumescence in China (Wang et al. 2022). In March of 2021, during a field survey in Xuanwei city, Yunnan province, China, some B. striata plants with symptoms of plant dwarfing and leaf yellowing were observed. Roots of diseased plants presented numerous galls, typical symptoms of root-knot nematodes (RKNs) infection. The diseased area was approximately 66667 m2, showing a patchy disease distribution pattern. To identify the species of RKNs, females and eggs were isolated from galled tissue, and second-stage juveniles (J2s) were collected from eggs hatched. Nematodes were identified through comprehensive morphological and molecular methods. The perineal pattern of females is round to ovoid with a flat or moderately high dorsal arch and has two conspicuous lateral line striae. Morphological measurements of females (n=20) included body length (L) = 702.9 ± 70.8 (556.2-780.2) μm, body width (BW) = 404.1 ± 48.5 (327.5-470.1) μm, stylet length = 15.5 ± 2.2 (12.3-18.6) μm, distance from base of stylet to dorsal esophageal gland opening (DGO) = 3.7 ± 0.8 (2.1-4.9) μm. The morphometrics of J2s (n=20), L = 438.4 ± 22.6 (354.1-464.8) μm, BW = 17.4 ± 2.0 (12.9-20.8) μm, stylet length = 13.5 ± 0.4 (13.0-14.2) μm, DGO = 3.2 ± 0.6 (2.6-4.7) μm, and hyaline tail terminus = 12.3 ± 1.9 (9.6-15.7) μm. These morphological characteristics were similar to the original descriptions of Meloidogyne javanica (Rammah and Hirschmann 1990). DNA extraction was done 60 times, each from a different single females following the method of Yang et al. (2020). Amplification of ITS1-5.8S-ITS2 region of rDNA and the coxI region of mtDNA was done by using primers 18S/26S (5'-TTGATTACGTCCCTGCCCTTT-3'/5'-TTTCACTCGCCGTTACTAAGG-3') (Vrain et al. 1992) and cox1F/cox1R (5'-TGGTCATCCTGAAGTTTATG-3'/5'-CTACAACATAATAAGTATCATG-3') (Trinh et al. 2019) respectively. The PCR amplification program followed the method described by Yang et al. (2021). The ITS1-5.8S-ITS2 gene sequence (768 bp, GenBank Accession No. OQ091922) showed 99.35-100% identical to the known sequences of M. javanica (GenBank Accession Nos. KX646187, MW672262, KJ739710, KP901063, MK390613). The coxI gene sequence (410 bp, OQ080070) showed 99.75%-100% identical to the known sequences of M. javanica (OP646645, MZ542457, KP202352, KU372169, KU372170). Furthermore, M. javanica species-specific primers Fjav/Rjav (5'-GGTGCGCGATTGAACTGAGC-3'/5'-CAGGCCCTTCAGTGGAACTATAC-3') were used for PCR amplification. An expected fragment of approximately 670 bp was obtained, which was identical to that previously reported for M. javanica (Zijlstra et al. 2000). To verify pathogenicity of this nematode on B. striata, six 1.6-year-old tissue culture seedings of B. striata were maintained in 10-cm-diameter × 9-cm-high plastic pots containing a sterilized mixed soil (humus soil: laterite soil: perlite=3:1:1), and each plant was inoculated with 1000 J2s hatched from eggs of M. javanica. Three non-inoculated B. striata were used as the negative controls. All plants were placed in a greenhouse at approximately 14～26 ℃. After 90 days, the inoculated plants presented symptoms of leaf yellowing, and the roots with root knots identical to those observed in the fields. The root gall rating was 2 according to the 0-5 RKNs rating scale (Anwar and McKenry, 2002) and the reproductive factor (RF= final population/initial population) was 1.6. No symptoms or nematodes were observed on control plants. The nematode was reisolated and identified as M. javanica by morphological and molecular methods as above. To our knowledge, this is the first report of infection of M. javanica on B. striata. The infection of this economically important medicinal plant with M. javanica could pose a great threat to B. striata production in China, and further research will be necessary to develop control strategies.

Targeting of CRISPR-Cas12a crRNAs into human mitochondria

Mitochondrial gene editing holds great promise as a therapeutic approach for mitochondrial diseases caused by mutations in the mitochondrial DNA (mtDNA). Current strategies focus on reducing mutant mtDNA heteroplasmy levels through targeted cleavage or base editing. However, the delivery of editing components into mitochondria remains a challenge. Here we investigate the import of CRISPR-Cas12a system guide RNAs (crRNAs) into human mitochondria and study the structural requirements for this process by northern blot analysis of RNA isolated from nucleases-treated mitoplasts. To investigate whether the fusion of crRNA with known RNA import determinants (MLS) improve its mitochondrial targeting, we added MLS hairpin structures at 3′-end of crRNA and demonstrated that this did not impact crRNA ability to program specific cleavage of DNA in lysate of human cells expressing AsCas12a nuclease. Surprisingly, mitochondrial localization of the fused crRNA molecules was not improved compared to non-modified version, indicating that structured scaffold domain of crRNA can probably function as MLS, assuring crRNA mitochondrial import. Then, we designed a series of crRNAs targeting different regions of mtDNA and demonstrated their ability to program specific cleavage of mtDNA fragments in cell lysate and their partial localization in mitochondrial matrix in human cells transfected with these RNA molecules. We hypothesize that mitochondrial import of crRNAs may depend on their secondary structure/sequence. We presume that imported crRNA allow reconstituting the active crRNA/Cas12a system in human mitochondria, which can contribute to the development of effective strategies for mitochondrial gene editing and potential future treatment of mitochondrial diseases.

Investigating the role of mitochondrial DNA D-loop variants, haplotypes, and copy number in polycystic ovary syndrome: implications for clinical phenotypes in the Chinese population.

The presence of genetic variations in mitochondrial DNA (mtDNA) has been associated with a diverse array of diseases. The objective of this study was to examine the correlations between mtDNA D-loop, its haplotypes, and polycystic ovary syndrome (PCOS) in the Chinese population, and the associations between mtDNA D-loop and symptoms of PCOS. The study also sought to determine whether the mtDNA copy number in Chinese patients with PCOS differed from that of individuals in the control group. Infertile individuals who only had tubal or male factor treatment were the focus of research by The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). mtDNA haplotypes were categorized using polymorphic D-loop sites. mtDNA D-loop, PCOS features, and mtDNA haplotypes were analyzed using R software to determine the strength of the association between the three. There are certain DNA haplotypes linked to PCOS. Microdroplet digital polymerase chain reaction (PCR) was used to determine the mtDNA copy number in a convenience sample of 168 PCOS patients and 83 controls. Among the research group, the majority of D-loop mutations were infrequent (frequency< 1%), with only 45 variants displaying a minimum allele frequency (MAF) of 5% or higher. No association was found between polymorphism loci in PCOS patients and body mass index (BMI). Noteworthy, C194T, 1A200G, 523delAC, and C16234T showed positive correlations with elevated LH/FSH levels. Additionally, specific polymorphic loci G207A, 16036GGins, and 16049Gins within the D-loop region of mtDNA potentially exerted a protective role in PCOS development. Conversely, no statistical significance was observed in the expression levels of C16291T and T489C. Chinese women with mtDNA haplotype A15 exhibited a decreased risk of developing PCOS. Moreover, a significant difference in mtDNA copy number was detected, with controls averaging 25.87 (21.84, 34.81), while PCOS patients had a mean of 129.91 (99.38, 168.63). Certain mtDNA D-loop mutations and haplotypes appear to confer protection against PCOS in Chinese women. In addition, elevated mtDNA copy number may serve as an indicator during early stages of PCOS.

Eastern Fennoscandian Wolf (&lt;i&gt;Canis lupus&lt;/i&gt; L.) under the Heavy Hunting Pressure: mtDNA Analysis as a Tool to Assess Hunting Impact on the Population-Genetic Structure

One of the most ancient aspects of human impact on the wild animals is hunting. The degree of human impact on one of the Eastern Fennoscandian wolf (Canis lupus L.) population based on the analysis of data on the population dynamics of the predator and its preys, “hunting bag” data, changes in the spatial-temporal structure and genetic characteristics, is shown. In the presented work, a genetic analysis of the control region mtDNA of the wolf of the Republic of Karelia (Russia) and the experimental territory (Kondopozhsky district of Karelia) was performed on a time slice of 10 years. The modern mtDNA haplotypic diversity of Russian Karelian and Finnish wolf population, in comparison with the general diversity characteristic for the species, is poor. In total, only two haplotypes common in Eurasia have been identified here, which is obviously explained by the history of the species – the stages of severe population decline.

The Acute Effects Of Exercise On Saliva-derived Regional Mtdna From Trained Runners

The Acute Effects Of Exercise On Saliva-derived Regional Mtdna From Trained Runners