NADH Dehydrogenase Subunit Research Articles

Molecular Markers Reveal a New and Possibly Threatened Species of Cnesterodon (Poeciliidae, Cnesterodontini) from the Upper Paraná River Basin, Brazil.

Cnesterodon comprises 10 valid species occurring in the major river basins of South America. Recent ichthyofaunistic studies in the Ivaí River basin, upper Paraná River system, suggested the existence of a possible new species, which was identified as Cnesterodon sp. based on morphological characters. Currently, the use of molecular tools has proved to be fundamental in aiding phylogenetics and cataloging biodiversity; therefore, in this study, we molecularly characterize a possible new species of Cnesterodon from the Ivaí River basin encoding the mitochondrial genes Cytochrome c Oxidase, subunit I (COI), and NADH dehydrogenase subunit 2 (ND2). The genetic differences found showed that this species really differs from the other Cnesterodon species, indicating that it is a distinct species, which is possibly already in serious danger of extinction since its habitat often suffers from human exploitation and its distribution is restricted to only two sites in the upper Ivaí River basin, but it has disappeared in one of them.

Plastome evolution and phylogenomics of Impatiens (Balsaminaceae)

This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538bp to 152,917bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.

A new species of the Cyrtodactylusbrevipalmatus group (Squamata, Gekkonidae) from the uplands of western Thailand.

An integrative systematic analysis recovered a new species of the Cyrtodactylusbrevipalmatus group from the uplands of Thong Pha Phum National Park, Kanchanaburi Province in western Thailand. Cyrtodactylusthongphaphumensissp. nov. is deeply embedded within the brevipalmatus group, bearing an uncorrected pairwise sequence divergence of 7.6-22.3% from all other species based on a 1,386 base pair segment of the mitochondrial NADH dehydrogenase subunit 2 gene (ND2) and adjacent tRNAs. It is diagnosable from all other species in the brevipalmatus group by statistically significant mean differences in meristic and normalized morphometric characters as well as differences in categorical morphology. A multiple factor analysis recovered its unique and non-overlapping placement in morphospace as statistically significantly different from that of all other species in the brevipalmatus group. The description of this new species contributes to a growing body of literature underscoring the high degree of herpetological diversity and endemism across the sky-island archipelagos of upland montane tropical forest habitats in Thailand, which like all other upland tropical landscapes, are becoming some of the most imperiled ecosystems on the planet.

Full-Length Transcriptome Profiling of Coridius chinensis Mitochondrial Genome Reveals the Transcription of Genes with Ancestral Arrangement in Insects.

Coridius chinensis (Hemiptera: Dinidoridae) is a medicinal insect. Its mitochondrial gene arrangement is consistent with that of Drosophila melanogaster and Erthesina fullo, the two insects with well-studied mitochondrial transcription. To investigate whether the structural consistency of mitochondrial genes leads to similarities in transcription and post-transcriptional processing, we improved the gene annotation and constructed a quantitative transcription map for the C. chinensis mitochondrial genome (mitogenome) using full-length transcriptome sequencing. The size of this mitogenome was 16,214 bp and the proposed model of mitochondrial transcription was similar to that of Drosophila. Both strands were nearly entirely transcribed except for the antisense genes downstream of trnS2 on N strand. The expression of cytochrome c subunit genes is higher than that of NADH-dehydrogenase subunit genes. The post-transcriptional cleavage process followed the "tRNA punctuation" model, and both the "reverse cleavage" model in Drosophila and "forward cleavage" model in E. fullo were found in C. chinensis. In addition, we found that long non-coding RNAs from the control region contained tandem repeats. Polyadenylation was performed after CCA triplet at the 3' end of tRNA. The isoform diversity of lrRNA was identified. Our study sheds light on the transcriptional regulation and RNA processing of insect mitogenomes with the putative ancestral gene arrangement.

Muscle fiber plasticity, stress physiology, and muscle transcriptome determine the inter-individual difference of swimming performance in the large yellow croaker (Larimichthys crocea)

Swimming performance is extremely important to critical activities of fishes, such as foraging, anti-predator, and migration. As one of primary stock enhancement fish species in China, it is imperative to study on swimming performance of the large yellow croaker (Larimichthys crocea). In the present study, the swimming performance of juvenile large yellow croaker was investigated, including the behavior, muscle morphology, stress physiology, and genetic mechanisms underlying the individual difference. Juveniles of the croaker were individually subjected to the critical swimming speed (Ucrit) test, and thereby divided into fast (36.47 cm/s) and slow (18.65 cm/s) groups. The juveniles in the fast group had significantly higher tail beat frequency, smaller muscle fiber diameter and more muscle fiber number, as well as lower plasma cortisol and corticotropin releasing hormone (CRH) levels than those in the slow group. Meanwhile, expression levels of hsp70 and pcna in the brain were significantly higher in the fast group than in the slow group, however no significant difference was observed in syt1a expression. Furthermore, the key genes and pathways involved in the swimming performance were assessed by mapping the white skeletal muscle transcriptome. We found that a total of 157 transcripts was differentially expressed between the fast and slow groups, enriched in oxidative phosphorylation, glycosaminoglycan biosynthesis, nicotinate and nicotinamide metabolism, cellular senescence, and cardiac muscle contraction pathways. A multitude of mitochondrial NADH dehydrogenase subunits and solute carrier family genes were especially related. In conclusion, we for the first time found that fish swimming performance directly links to muscle fiber plasticity, stress physiology, and molecular base divergence in the large yellow croaker. The present results lay a foundation for ethological-character-based selective breeding for the large yellow croaker in the regards of swimming performance.

Reassessment of the subspecific status of the Australian Wet Tropics yellow-bellied glider, Petaurus australis

The Wet Tropics (WT) population of the yellow-bellied glider Petaurus australis Shaw, 1791 in North Queensland is listed as Endangered at the state and national level, but its taxonomic classification is currently uncertain. Here we expand on previous genetic and morphological analyses of the WT population with additional samples and genetic loci to re-assess its subspecific status. Phylogenetic analyses of the mitochondrial NADH dehydrogenase subunit 4 (ND4) gene showed that the WT population formed a reciprocally monophyletic group relative to a group comprising P. australis from its remaining distribution in Australia. The genetic distinction of the WT population was further corroborated by analyses of the nuclear gene von Willebrand factor. Molecular clock analyses of combined ND2–ND4 data suggested that the WT population has been isolated from neighbouring populations in southern Queensland over multiple ice age cycles. Morphological analyses show that the WT gliders are smaller, with proportionally shortened faces, and have paler bellies compared to southern yellow-bellied gliders. We, therefore, propose that the WT population be recognised as a distinct subspecies which we herein describe. This taxonomic reassessment of P. australis has important implications for the ongoing conservation management of the WT population and yellow-bellied gliders throughout Australia.

High killing rate of nematode and promotion of rice growth by synthetic volatiles from Bacillus strains due to enhanced oxidative stress response.

The plant parasitic nematode Aphelenchoides besseyi is a major pest that poses serious threats to different vegetables and crop plants. In the present study, volatiles isolated from Bacillus spp. were utilized as green biocontrol agents to overcome nematodes. In in vitro experiment, Bacillus spp. GBSC56, SYST2, and FZB42 showed the strongest nematicidal activity with killing rates of 80.78%, 75.69%, and 60.45%, respectively, as compared with control. The selected synthetic volatile organic compounds (VOCs), namely albuterol, benzaldehyde (BDH), 1,2-benzisothiazol-3(2H)-one (1,2-HIT), dimethyl disulfide (DMDS), 2-undecanone (2-UD), and 1,3-propanediole (1,3-PD), exhibited strong nematicidal activity, with A. besseyi killing rate of 85.58%, 82.65%, 81.75%, 80.36%, 84.45%, and 82.36%, respectively, at 400 μg/mL. Microscopic analysis proved that the rapid mortality was due to the production of reactive oxygen species (ROS). Molecular docking attributed this ROS production to the nematicidal effect of synthetic VOCs on NADH DEHYDROGENASE SUBUNIT 2, which is known to play a critical role in the suppression of ROS in nematode models. In a greenhouse experiment, the Bacillus strains GBSC56, SYST2, and FZB42 and their synthetic VOCs significantly improved the physiological parameters in terms of growth promotion traits. In addition, selected genes related to growth promotion and defense genes showed a significant upregulation of their expression in rice seedlings treated with those synthetic VOCs. Overall, these findings revealed that the selected Bacillus strains and their synthetic VOCs possess high potential against A. besseyi. Moreover, this study also sheds new light on the mechanisms by which specific Bacillus nematicidal VOCs influence important genes involved in rice plant growth promotion and could effectively be used to suppress plant parasitic nematodes.

Loss of plastid ndh genes in an autotrophic desert plant

Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.

Характеристика спектра миссенс-замен в митохондриальных генах субъединиц НАДН дегидрогеназы для гаплогрупп мтДНК, распространенных в Северной Евразии

На основе анализа последовательностей митохондриальной ДНК (мтДНК), депонированных в базах данных, исследован спектр аминокислотной изменчивости субъединиц комплекса I дыхательной цепи, кодируемых мтДНК, в зависимости от принадлежности к различным гаплогруппам мтДНК. Установлено, что около 20% аминокислот являются полиморфными в исследованном наборе последовательностей, и для 30% полиморфных аминокислот зарегистрировано более одного мутационного события (гомоплазия). Выявлено действие отрицательного отбора для некоторых генов комплекса I в гаплогруппах мтДНК, распространенных преимущественно в северных широтах. Показано, что индекс консервативности аминокислотных замен в генах комплекса I ниже, чем в других генах мтДНК, а для гена ND1 - выше, чем для других генов комплекса I. Для замен в «северных» гаплогруппах мтДНК по сравнению с распространенными в южных широтах выявлены более высокие средние значения показателя MutPred, отражающего величину эффекта замены аминокислоты на структуру и функцию белка и показателя mtDNA selection score. Based on the analysis of mitochondrial DNA sequences deposited in databases, the spectrum of amino acid variability of the mtDNA-encoded subunits of the respiratory chain complex I was studied depending on mtDNA haplogroup affiliations. It was found that about 20% of amino acids were polymorphic in the studied dataset, and for 30% of polymorphic amino acids more than one mutational event (homoplasy) was registered. The effect of negative selection was revealed for some complex I genes in mtDNA haplogroups, distributed mainly in Northern Eurasia. It has been shown that the conservation index for amino acid substitutions in complex I genes is lower than in other mtDNA genes, and for the ND1 gene this index is higher than for other complex I genes. For the MutPred index and the mtDNA selection score, which reflect the effect of amino acid substitution on the structure and function of the protein, higher average values were registered in the “Northern” mtDNA haplogroups, comparing to the “Southern” haplogroups.

Genetic Polymorphism and Phylogenetics of Aedes aegypti from Sudan Based on ND4 Mitochondrial Gene Variations.

This study investigated the genetic differences between Aedes aegypti subspecies (Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf)) from Sudan using the NADH dehydrogenase subunit 4 (ND4) mitochondrial gene marker. Nineteen distinct haplotypes of the ND4 were identified in female Aedes aegypti mosquitoes from the study sites. The phylogenetic relationship of the 19 ND4 haplotypes was demonstrated in a median-joining haplotype network tree with Aaa and Aaf populations found to share three haplotypes. The genetic variance (Pairwise FST values) was estimated and found to range from 0.000 to 0.811. Isolation by distance test revealed that geographical distance was correlated to genetic variation (coefficient value (r) = 0.43). The Polar maximum likelihood tree showed the phylogenetic relationship of 91 female Aaa and Aaf from the study sites, with most of the Aaf haplotypes clustered in one group while most of the Aaa haplotypes gathered in another group, but there was an admixture of the subspecies in both clusters, especially the Aaa cluster. The Spatial Analysis of Molecular Variance (SAMOVA) test revealed that the eight populations clustered into two phylogeographic groups/clusters of the two subspecies populations. The 2 Aedes aegypti subspecies seemed not to be totally separated geographically with gene flow among the populations.

Analysis of Porcine DNA in Gelatine Products using SYBR Green Real Time Polymerase Chain Reaction for Halal Verification

Real-time PCR was employed in this study to determine whether gelatine items from nearby marketplaces contained porcine DNA. The mitochondrial NADH dehydrogenase subunit 5 (MT-ND5) gene from pigs (Sus scrofa) was the subject of oligonucleotide primer design; the forward and the reverse primer sequences produced 161bp amplicon. SYBR Green fluorescent dye was used to detect swine DNA in samples of 22 different types of gelatine products, 12 of which had labels identifying their sources and indicating their certification as Halal, and the remaining 10 had neither labels nor certification information. The 40 cycles of positive amplication with a Ct value of 19.81 served as the criterion for determining the specificity of the primers. In this work, the detection threshold for porcine DNA is set at 0.001 µg/ml. The efficiency of the PCR in this study is 91.72%, and the R2 is 0.9985, which indicates good efficiency. The 12 labelled products exhibit positive amplifications for porcine gelatine products while exhibiting negative amplifications for both bovine and fish gelatine products in labelled samples. Nine out of the ten samples of gelatine products that were tested had positive amplifications without source or Halal labelling.

Study of Genetic Diversity of Native Indonesian Catfish Based on Nucleotide Sequences of the ND1 Gene

One of the native catfish to Indonesia is the baung fish (Hemibagrus). Baung fish are found in rivers in Sumatra, Kalimantan and Java. The catfish population is declining, thus conservation is needed to prevent extinction. To conduct an effective conservation efforts, molecular studies are needed to confirm the fish species from the three islands. Mitochondrial DNA is one of the markers that is often used to see the lineage and kinship of animals for conservation purposes. The purpose of this study is to determine the genetic diversity of the NADH Dehydrogenase Subunit I (ND1) gene catfish from each of these locations, can be used as a genetic marker. Samples were obtained from their natural habitat, namely Magelang (5), Palembang (3), Riau (2), Samarinda (2), 2 from Sintang, and 3 from Banjarmasin. The DNA of the fish sample was then isolated and then used as a template for amplification of DNA fragments using PCR techniques. Amplikon (PCR product) was then purified by gel extraction and then sequenced to determine the DNA sequence. The potential of DNA sequences as catfish genetic markers was proven by analyzing genetic diversity between species using the MEGA version 7.0 program (Kumar et al., 2016). The sequencing results 972 nucleotides composing the ND gene, and found differences in 268 nucleotide sites and 47 amino acid sites. Based on the nucleotide sequence of the ND1 gene, catfish from the Progo river (Magelang, Central Java), the Musi river (Palembang, Sumatra), the Kampar river (Riau), the Kapuas river (Sintang, Kalimantan), the Martapura river (Banjarmasin), the Mahakam river (Kalimantan) is included in the Hemibagrus sp.; catfish from the Elo river (Magelang, Central Java) belongs to the genus Mystus sp.; catfish from the Bengawan Solo river (Bojonegoro, East Java) belongs to the Pangasius sp.

Effects of bulk and nano-ZnO particles on functioning of photosynthetic apparatus in barley (Hordeum vulgare L.)

The functioning of the photosynthetic apparatus in barley (Hordeum vulgare L.) after 7-days of exposure to bulk (b-ZnO) and nanosized ZnO (n-ZnO) (300, 2000, and 10,000 mg/l) has been investigated. An impact on the amount of chlorophylls, photosynthetic efficiency, as well as the zinc accumulation in chloroplasts was demonstrated. Violation of the chloroplast fine structure was revealed. These changes were generally more pronounced with n-ZnO exposure, especially at high concentrations. For instance, the chlorophyll deficiency under 10,000 mg/l b-ZnO treatment was 31% and with exposure to 10,000 mg/l n-ZnO, the chlorophyll deficiency was already 52%. The expression analysis of the photosynthetic genes revealed their different sensitivity to b-ZnO and n-ZnO exposure. The genes encoding subunits of photosystem II (PSII) and, to a slightly lesser extent, photosystem I (PSI) showed the highest suppression of transcriptional levels. The mRNA levels of the subunits of cytochrome-b6f, NADH dehydrogenase, ribulose-1,5-bisphosphate carboxylase and ATP synthase, which, in addition to linear electron flow (LEF), participate in cyclic electron flow (CEF) and autotrophic CO2 fixation, were more stable or increased under b-ZnO and n-ZnO treatments. At the same time, CEF was increased. It was assumed that under the action of b-ZnO and n-ZnO, the processes of LEF are disrupted, and CEF is activated. This allows the plant to prevent photo-oxidation and compensate for the lack of ATP for the CO2 fixation process, thereby ensuring the stability of photosynthetic function in the initial stages of stress factor exposure. The study of photosynthetic structures of crops is important from the point of view of understanding the risks of reducing the production potential and the level of food security due to the growing use of nanoparticles in agriculture.

A new species of feather-tailed leaf-toed gecko, Kolekanos Heinicke, Daza, Greenbaum, Jackman, Bauer, 2014 (Squamata, Gekkonidae) from the poorly explored savannah of western Angola.

We here describe a new species of feather-tailed leaf-toed gecko, Kolekanos, from southern Benguela Province, Angola, based on morphological and osteological evidence, supported by phylogenetic analysis of mitochondrial data. The new species adds to the rapidly growing and newly-recognised endemic biodiversity of Angola, doubling the number of Kolekanos species, breaking the pattern observed within other closely-related African members of a clade of circum-Indian Ocean leaf-toed geckos - Ramigekko, Cryptactites and Afrogecko - all of which are presently monotypic. The new species is easily distinguished from K.plumicaudus, based on spine-like (as opposed to feather-like) scales on the margins of the original tail. Phylogenetic analyses also recovered the new taxon as monophyletic, with a well-supported sister relationship to K.plumicaudus, from which it differs by a substantial 24.1% NADH-dehydrogenase subunit 2 mitochondrial gene uncorrected p-distance.

Dispersal direction of Malaysian Fasciola gigantica from neighboring southeast Asian countries inferred using mitochondrial DNA analysis.

Fasciola gigantica and hybrid Fasciola flukes, responsible for the disease fasciolosis, are found in Southeast Asian countries. In the present study, we performed molecular species identification of Fasciola flukes distributed in Terengganu, Malaysia using multiplex PCR for phosphoenolpyruvate carboxykinase (pepck) and PCR-restriction fragment length polymorphism (RFLP) for DNA polymerase delta (pold). Simultaneously, phylogenetic analysis based on mitochondrial NADH dehydrogenase subunit 1 (nad1) was performed for the first time on Malaysian Fasciola flukes to infer the dispersal direction among neighboring countries. A total of 40 flukes used in this study were identified as F. gigantica. Eight nad1 haplotypes were identified in the F. gigantica population of Terengganu. Median-joining network analysis revealed that the Malaysian population was related to those obtained from bordering countries such as Thailand and Indonesia. However, genetic differentiation was detected using population genetics analyses. Nevertheless, the nucleotide diversity (π) value suggested that F. gigantica with the predominant haplotypes was introduced into Malaysia from Thailand and Indonesia. The dispersal direction suggested by population genetics in the present study may not be fully reliable since Fasciola flukes were collected from a single location in one state of Malaysia. Further studies analyzing more samples from many locations are required to validate the dispersal direction proposed herein.

Development and validation of two environmental DNA assays for American Eel (Anguilla rostrata)

AbstractWe developed and validated two species‐specific qPCR markers to detect American Eel environmental DNA. Marker validation included assay design, specificity and sensitivity testing, and in vivo laboratory and field experiments. Markers AME1 and AME2 targeted 116 and 129 bp fragments of the mitochondrial NADH dehydrogenase subunit 2 and cytochrome b genes, respectively. Markers were 94%–100% homologous for all 49 aligned American Eel sequences. Specificity tests, with known DNA obtained from 149 individuals spanning 81 fish species, amplified DNA derived from American Eel tissue exclusively. Each marker also had high sensitivity with LOD and LOQ values of 2.8–50 copies. For each marker, pilot testing of American Eel in aquaria at increasing densities (n = 0, 1, 5, 10 eels) showed a significant (p < 0.03) negative relationship between mean qPCR cycle threshold value and number of eels per tank. Our in situ testing of water samples collected from 35 sites on the East Coast (from as far south as Maryland to as far north as Maine) revealed that sites known to contain populations of American Eel (n = 11) were all positive for American Eel DNA, while sites where American Eel were presumed absent (n = 24) failed to amplify American Eel DNA. In three cases, our assays produced positive detections in the lower portion of a watershed but failed to detect American Eel upstream of a presumed impassible barrier in each of the same watersheds (all internal positive controls indicated no evidence of PCR inhibition in our field samples and all negative controls indicated no evidence of contamination). Our encouraging results of in vitro and in situ validation demonstrate the utility of using eDNA as a tool to aid in American Eel conservation efforts.

Hidden diversity of rock geckos within the Cnemaspissiamensis species group (Gekkonidae, Squamata): genetic and morphological data from southern Thailand reveal two new insular species and verify the phylogenetic affinities of C.chanardi and C.kamolnorranathi.

Two new insular rock geckos in the genus Cnemaspis are described from Ko Samui in Surat Thani Province and Ko Similan in Phang-nga Province, southern Thailand, based on a combination of morphological and mitochondrial NADH dehydrogenase subunit 2 (ND2) data. Both new species represent divergent lineages within the Cnemaspissiamensis species group. Cnemaspissamui sp. nov. is distinguished from other species in the group by having eight or nine supralabial and infralabial scales; 5-8 pore-bearing precloacal scales in males, pores rounded; 25-27 paravertebral tubercles, arranged randomly; 22-25 subdigital lamellae under 4th toe; enlarged median subcaudal scale row present; gular region, abdomen, limbs and subcaudal region yellowish only in males, and uncorrected pairwise divergences of 8.86-26.83% from all other species in the C.siamensis species group. Cnemaspissimilan sp. nov. is distinguished from other species in the group by having eight or nine supralabial and seven or eight infralabial scales; one pore-bearing precloacal scale in males, pore rounded; 24 or 25 paravertebral tubercles, arranged randomly; 23 or 24 subdigital lamellae under 4th toe; no enlarged median subcaudal scale row; pale yellow reticulum on head, neck, flanks, belly and limbs in male only, and uncorrected pairwise divergences of 9.34-27.11% from all other species in the C.siamensis species group. Cnemaspissamui sp. nov. is found along granitic rocky stream outcrops of Hin Lad Waterfall, Ko Samui, Gulf of Thailand, while Cnemaspissimilan sp. nov. occurs in granitic rocky outcrops near Ao Nguang Chang Bay, Ko Similan, Andaman Sea. The phylogenetic analyses confirmed that C.chanardi and C.kamolnorranathi are also nested within the C.siamensis species group, as previously hypothesized from morphology and color pattern characters.

Population structure, molecular characterization, and phylogenetic analysis of Fasciola gigantica from two locations in Uganda.

Fasciola gigantica is a major pathogen that causes fasciolosis in Africa. A recent study in Uganda demonstrated that Fasciola flukes were present in 65.7% of slaughtered cattle. However, molecular identification of Fasciola species has not yet been performed in the country. In the present study, 292 Fasciola flukes were collected from Kampala and Gulu, Uganda. The samples were identified as F. gigantica using a multiplex polymerase chain reaction (PCR) assay for phosphoenolpyruvate carboxykinase (pepck) and a PCR-restriction fragment length polymorphism (RFLP) assay for DNA polymerase delta (pold). A significant genetic difference between F. gigantica obtained from cattle slaughtered at Kampala and Gulu was observed by analyzing the mitochondrial markers NADH dehydrogenase subunit 1 (nad1) and cytochrome C oxidase subunit 1 (cox1). Fasciola collected from Gulu had a more diversified population than that collected from Kampala, probably because of differences in livestock management systems. One of the possible reasons for this observation is that cattle slaughtered in Gulu were reared under an extensive communal grazing system, which is suitable for maintaining parasite diversity, whereas cattle slaughtered in Kampala mainly originated from fenced/closed farms, which limits parasite diversity. However, the cause of the difference between these two locations was not clearly defined by the results of this study. The F. gigantica population from Uganda was related to that obtained from Zambia. A star-like phylogeny was detected in a median-joining network analysis, which indicated rapid population expansion and suggested that the F. gigantica populations from both countries are maintained by domestic ruminants in eastern Africa. Interestingly, the F. gigantica population from Uganda was not related to those from Egypt and Nigeria. The results of the present study suggest that F. gigantica populations in African countries are indigenous to each country or region.

Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability

BackgroundCytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome. However, the relationship between mitochondrial function and sterility stability is largely unknown.ResultsIn this study, we determined the ratio of plants carrying exerted anthers in the population of two CMS-S subtypes. The subtype with a high ratio of exerted anthers was designated as CMS-Sa, and the other with low ratio was designated as CMS-Sb. Through next-generation sequencing, we assembled and compared mitochondrial genomes of two CMS-S subtypes. Phylogenetic analyses revealed strong similarities between the two mitochondrial genomes. The sterility-associated regions, S plasmids, and terminal inverted repeats (TIRs) were intact in both genomes. The two subtypes maintained high transcript levels of the sterility gene orf355 in anther tissue. Most of the functional genes/proteins were identical at the nucleotide sequence and amino acid sequence levels in the two subtypes, except for NADH dehydrogenase subunit 1 (nad1). In the mitochondrial genome of CMS-Sb, a 3.3-kilobase sequence containing nad1-exon1 was absent from the second copy of the 17-kb repeat region. Consequently, we detected two copies of nad1-exon1 in CMS-Sa, but only one copy in CMS-Sb. During pollen development, nad1 transcription and mitochondrial biogenesis were induced in anthers of CMS-Sa, but not in those of CMS-Sb. We suggest that the impaired mitochondrial function in the anthers of CMS-Sb is associated with its more stable sterility.ConclusionsComprehensive analyses revealed diversity in terms of the copy number of the mitochondrial gene nad1-exon1 between two subtypes of CMS-S maize. This difference in copy number affected the transcript levels of nad1 and mitochondrial biogenesis in anther tissue, and affected the reversion rate of CMS-S maize. The results of this study suggest the involvement of mitochondrial robustness in modulation of sterility stability in CMS-S maize.

Comparison of mitochondrial genetic variation of Taenia hydatigena cysticerci from China and Mongolia.

Parasitic infection is one of the many challenges facing livestock production globally. Cysticercosis tenuicollis is a common parasitic disease in domestic and wild ruminants (intermediate host) caused by the larval stage of Taenia hydatigena that primarily infects dogs (definitive host). Although genetic studies on this parasite exist, only a few describe the genetic variation of this parasite in Mongolia. Our aim was thus, to identify the mitochondrial differences in ovine isolates of Cysticercus tenuicollis entering China from Mongolia and comparison with existing Chinese isolates from sheep and goats based on the recently described PCR-RFLP method and mitochondrial genes of NADH dehydrogenase subunit 4 (nad4) and the NADH dehydrogenase subunit 5 (nad5). Sixty-nine isolates were collected during routine veterinary meat inspections from sheep that originated from Mongolia, at the modern slaughterhouses in Erenhot City, Inner Mongolia. Additional 114 cysticerci were also retrieved from sheep and goats from northern (Inner Mongolia Autonomous Region, Ningxia Hui Autonomous Region, and Gansu Province), western (Tibet Autonomous Region), and southern (Jiangxi Province and Guangxi Province) China. The PCR-RFLP approach of the nad5 showed nine mitochondrial subclusters A1, A2, A3, A5, A8, A9, A10, A11, and B of T. hydatigena isolates from sheep and goats from Mongolia and China. Meanwhile, haplogroup A1 RFLP profile was more widespread than other variants. These data supplements existing information on the molecular epidemiology of T. hydatigena in China and Mongolia and demonstrate the occurrence of similar genetic population structures in both countries.