Search Results (395)

Carassius auratus var. suogu, an endemic fish in southern China, is a natural triploid crucian carp mutant. In this study, the characteristics of mitochondrial DNA sequences were analyzed to understand their taxonomic status and genetic background at the gene level. The complete mitochondrial genome of C. auratus var. suogu (length, 16,580 bp) comprises 37 genes (13 protein-coding genes, 22 transfer RNA (tRNAs) genes, and 2 ribosomal RNA (rRNAs) genes) and a non-coding control region. The RSCU of the mtDNA of Carassius was similar. Ka/Ks analyses showed the ND4 gene had the highest evolutionary rate. Moreover, the whole mitogenome sequences and D-loop region were employed to examine phylogenetic relationships among C. auratus var. suogu and other closely related species. The result indicated that Carassius auratus suogu var clustered with Carassius auratus auratus and divided Carassius into four clades, providing new insights and data support for the taxonomic status of Carassius. Full article

In order to investigate the infection status of Cryptosporidium in O. curzoniae and B. grunniens in Zoige County, Sichuan Province, fecal samples from B. grunniens and gastrointestinal contents from captured O. curzoniae were collected between March and December 2023 from five townships (Dazhasi, Axi, Hongxing, Tangke, and Maixi). Genomic DNA was extracted, and nested PCR targeting the small subunit (SSU) rRNA gene of Cryptosporidium was performed. PCR-positive products were sequenced, trimmed, aligned, and subjected to phylogenetic analysis to determine species and genotypes. A total of 242 samples were obtained, of which 20 were Cryptosporidium SSU rRNA-positive, yielding an overall detection rate of 8.3% (20/242). The detection rates of O. curzoniae and B. grunniens were 7.0% (8/114) and 9.4% (12/128), respectively. Among the five sampling sites, Maixi town exhibited the highest detection rate (32.4%, 11/44), followed by Hongxing town (15.2%, 7/46) and Tangke town (4.6%, 2/44). Phylogenetic analysis detected an unidentified Cryptosporidium sp. in O. curzoniae, while C. bovis (n = 10) and C. ryanae (n = 2) were detected in B. grunniens. These findings demonstrate that Cryptosporidium infections are present in both O. curzoniae and B. grunniens in Zoige County, with notable differences in infection rates and species composition. Continued surveillance of Cryptosporidium in local livestock and wildlife is warranted to provide critical data for regional public health management. Full article

Castor fiber birulai is a subspecies of the Eurasian beaver that has a relatively small population size compared to other Castor subspecies. There is limited genetic research on this subspecies. In this study, mitochondrial cytochrome b (Cytb) and D-loop sequences were analysed in genetic samples obtained from 19 individuals residing in the Buergen River Basin, Xinjiang, China. The Cytb region presented a single haplotype, whereas three haplotypes were identified in the D-loop region. The genetic diversity within the Chinese population was low (D-loop Hd = 0.444; Pi = 0.0043), markedly lower than that observed in other geographical populations of C. fiber. Phylogenetic reconstructions and haplotype network analyses revealed substantial genetic differentiation between C. f. birulai and other Eurasian lineages (Fst > 0.95), supporting the status of C. f. birulai as a distinct evolutionary lineage. Although the genetic distance between the Chinese and Mongolian populations was relatively small (distance = 0.00269), significant genetic differentiation was detected (Fst = 0.67055), indicating that anthropogenic disturbances—such as hydraulic infrastructure and fencing along the cross-border Bulgan River—may have impeded gene flow and dispersal. Demographic analyses provided no evidence of recent population expansion (Fu’s Fs = 0.19152), suggesting a demographically stable population. In subsequent studies, we recommend increasing nuclear gene data to verify whether the C. f. birulai population meets the criteria for Evolutionarily Significant Unit classification, and strengthening cross-border protection and cooperation between China and Mongolia. Full article

Apples (Malus domestica), one of Iran’s oldest cultivated fruit crops, hold considerable economic importance. In this study, 170 apple leaf samples representing various commercial cultivars were collected across the country. RT-PCR screening targeted five common apple-infecting viruses and two viroids: apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV), apple green crinkle-associated virus (AGCaV), apple mosaic virus (ApMV), apple scar skin viroid (ASSVd), and hop stunt viroid (HSVd). To identify additional or novel agents, 40 RT-PCR-negative samples were pooled into two composite groups and analyzed using next-generation sequencing (NGS). NGS was also performed on individual samples with mixed infections to retrieve full genomes. RT-PCR confirmed the presence of ACLSV, ASPV, ASGV, AGCaV, ApMV, and HSVd. NGS further revealed three additional pathogens: citrus concave gum-associated virus (CCGaV), apple hammerhead viroid (AHVd), and apricot vein clearing-associated virus (AVCaV), which were subsequently detected across the collection by RT-PCR. AGCaV was most prevalent (47.6%), followed by ACLSV (45.8%), HSVd (27.6%), AVCaV (20.5%), ASGV (17%), AHVd (15.2%), ASPV (14.1%), CCGaV (4.7%), and ApMV (3.5%). Mixed infections occurred in 67% of samples. Phylogenetic analysis based on CP genes (ACLSV, ASGV, AGCaV) and full genomes (AVCaV, AHVd) clustered Iranian isolates together, suggesting a common origin. This is the first report in Iran of AGCaV, CCGaV, ApMV, and AVCaV in apple, and notably, the first global report of AVCaV in a non-Prunus host. The findings provide the first comprehensive assessment of the sanitary status of apple trees in Iran. Full article

The Catostemma clade comprises three genera: Aguiaria, Catostemma, and Scleronema. These genera are representatives of the tribe Adansonieae, and are part of the subfamily Bombacoideae of the Malvaceae family. Taxonomic studies of these genera are scarce and limited to isolated publications of new species or regional floras. We reviewed their taxonomy, morphology, and geography, and assessed gaps in our knowledge of this group. We carried out a bibliographic survey, an analysis of herbarium collections, and collected new material in Brazilian forests. Here, we provide an identification key, nomenclatural revisions, morphological descriptions, taxonomic comments, geographic distribution maps, illustrations, and analyses of the conservation status for all species. We also discuss probable synapomorphies of the clade, to advance our understanding of phylogenetic relationships within the Adansonieae tribe of Bombacoideae. In total, we recognize 16 species: 1 Aguiaria, 12 Catostemma, and 3 Scleronema, of which 7 are endemic to Brazil, 1 to Colombia, and 1 to Venezuela. Two species are ranked as Critically Endangered (CR), and four as Data Deficient (DD). Full article

This study investigates the taxonomic status, phylogenetic relationships, and genetic diversity of Japanese chestnut (Castanea crenata Siebold & Zucc.) in Liaodong, China, and across East Asia. Additionally, it evaluates core germplasm resources through cluster and population structure analyses using simple sequence repeat (SSR) marker data from 13 Castanea henryi, 18 Castanea seguinii, and 27 Castanea mollissima, and 142 Japanese chestnut resources. The results show that the East Asian Castanea genus forms a monophyletic group with distinct interspecific boundaries. Japanese chestnut and two varieties/lines of C. seguinii (187 and 170) form a sister clade, indicating a close phylogenetic relationship. All Japanese chestnut resources are divided into two branches, with considerable admixture. The genetic diversity analysis revealed that the 142 Japanese chestnut varieties/lines collectively possessed 141 allelic loci, with genetic distances (GDs) ranging from 0.429 to 0.880 with an average of 0.740. Based on unique characteristics, seven resources with distinctive features were selected as mandatory. A total of 41 core germplasm resources were finally determined using the simulated annealing method. The comparative analysis revealed that, aside from a notable difference in polymorphic information loci, the core germplasm and original germplasm showed no significant differences in other genetic diversity parameters. This indicates that the 41 core germplasm resources effectively preserve the genetic diversity of the original germplasm and have been influenced by artificial selection. This study provides a scientific basis for conserving and using C. crenata germplasm resources. Full article

Background: Clinical features of asthma are associated with differences in the lower airway microbiome. However, knowledge is limited on whether airway microbiota composition differs between individuals residing in different geographic regions and if asthma-associated differences in lower airway microbiota are similar between distinct populations. Methods: Existing 16S rRNA gene sequence data, generated from sputum collected from adults with or without asthma (n = 74) from two single-center cohort studies in the U.S. and United Arab Emirates, were re-processed for merged computational analysis using standard available tools. Potential differences between study sites, asthma status and specific clinical factors (inhaled corticosteroid use, ICS; obesity) were examined. Results: Differences in sputum bacterial composition, assessed by alpha- and beta-diversity measures, were associated with study site. Despite this, asthma-related differences were discerned in both cohorts. Specifically, sputum microbiota of asthmatic patients on ICS treatment displayed reduced bacterial phylogenetic diversity, compared to those not on ICS treatment (p = 0.006). Sputum bacterial composition also differed by obesity status (unweighted Unifrac distance PERMANOVA, p = 0.004). Specific genera were identified in both cohorts that were differentially enriched between obese vs. non-obese subjects, including Rothia and Veillonella (obesity-associated) and Campylobacter (non-obesity-associated). Conclusions: Our findings suggest clinical factors associated with differences in the lower airway microbiome in asthma may transcend variation related to geographic area of residence. Full article

The number of Fritillaria species native to the Alps has long been debated, and observational biases due to the short flowering periods and the scattered distributions of endemic Fritillaria populations along the mountain range have probably made the task of botanists more complicated. Moreover, previous phylogenetic studies in Fritillaria have considered alpine taxa only marginally. To test species boundaries within the F. tubaeformis species complex and to study their phylogenetic relationships, intra- and inter-specific genetic variability of sixteen samples belonging to four Fritillaria species was carried out in different localities of the Maritime and Ligurian Alps, with extensions to the rest of the Alpine arc. The combined use of five plastid DNA markers (matK, ndhF, rpl16, rpoC1, and petA-psbJ) and nrITS showed that F. tubaeformis and F. burnatii are phylogenetically independent taxa, fully confirming morphological and morphometric divergences and, that F. burnatii is not related phylogenetically to the central European F. meleagris. Our phylogenetic study also supports the separation of F. tubaeformis from F. moggridgei, pointing to environment/ecological constraints or reproductive barriers as possible causes of their distinct evolutionary status. Our analysis also showed that the mountain endemic F. involucrata is not closely related to F. tubaeformis, contrasting with previous studies. The phylogenetic analysis of the nrITS region supports a close relationship between F. burnatii and F. moggridgei, but with low statistical support. Full article

Between 2018 and 2019, Israel experienced one of its largest measles outbreaks in recent decades, with over 4300 reported cases and more than 100 documented importation events. Despite high national vaccination coverage, the prolonged nature of the outbreak posed a risk to the country’s measles elimination status. Traditional epidemiological investigations and genotyping based on the N450 region lacked sufficient resolution to differentiate between sustained local transmission and multiple independent introductions. To address this, we performed whole-genome sequencing on 123 measles virus samples representing both imported and locally acquired cases from diverse geographic regions. Phylogenetic analysis revealed multiple, distinct transmission chains, several of which could be linked to separate importation events. The MF non-coding region (MF-NCR) not only showed the highest genetic variability, but also contained many of the phylogenetic cluster-defining mutations, though informative changes were found throughout the whole genome. These findings demonstrate the value of whole-genome sequencing in resolving complex transmission dynamics and highlight the importance of integrating genomic epidemiology into routine measles surveillance. Such integration can enhance outbreak investigations and better inform public health responses to protect elimination status. Full article

Background: Siphonaria is a genus of false limpets belonging to the Gastropoda class. Only two species of this genus have been described with mitochondrial genomes. Moreover, the codon usage patterns and factors influencing them have not been studied. This study aims to expand the mitochondrial genome data of this genus and clarify the codon usage patterns. Methods: The complete mitochondrial genome of Siphonaria japonica was sequenced using next-generation sequencing. The gene arrangement and phylogenetic status were compared with Siphonaria gigas and Siphonaria pectinata. The codon usage bias of the three mitochondrial genomes was analyzed based on the relative synonymous codon usage (RSCU), the effective number of codons (ENC) plot, the parity rule 2 (PR2)-bias plot, and neutrality plot analyses. Results: The gene arrangement and maximum-likelihood phylogenetic tree support a close relationship between S. japonica and S. pectinata. The codon usage bias analysis indicated that the codon usage bias of mitochondrial PCGs in the three species was primarily influenced by natural selection. Conclusions: This study offers significant evolutionary insights into the phylogenetic relationships and molecular adaptation strategies among Siphonaria species. Full article

Canine distemper virus (CDV) is a highly contagious pathogen and causes a fatal systemic disease in domestic dogs and wild carnivores worldwide. Despite CDV infections being monitored globally, studies on CDV in Vietnam seem to be limited. This study, therefore, investigated the epidemiological, clinical, and molecular characteristics of CDV in the Mekong Delta (MD) region of Vietnam. A total of 6687 ocular/nasal swabs were collected from CDV-suspected dogs across seven cities/provinces. CDV infection was detected in 6.19% (414 dogs) of suspected dogs using a commercially available rapid kit, with infection associated with age, roaming status, and vaccination status. Hematological and blood biochemical analysis of CDV-infected dogs revealed anemia, leukopenia, neutrophilia, thrombocytopenia, a slight increase in aspartate aminotransferase (AST) levels, and a significant increase in blood urea nitrogen (BUN) levels. Molecular characterization of partial hemagglutinin (H) and fusion (F) genes exhibited high nucleotide and amino acid homology with the Asia-1 genotype. Phylogenetic analysis confirmed that the field sequences were clustered into the Asia-1 genotype together with the neighboring countries. These findings provide important insights into the current epidemiological, clinical, and molecular features of CDV circulating in Vietnam. Full article

Background/Objectives: Aurochs (Bos primigenius), one of the earliest and largest herbivores domesticated by humans, were widely distributed in Eurasia and North Africa during the Pleistocene and Holocene. Studies of aurochs in China have focused mainly on the Northeastern region. Previous studies have suggested that haplogroup C is a haplogroup unique to China, but recent studies have shown that this is not the case. We have compiled all data on haplogroup C to revisit the classification of the aurochs haplogroup C. Methods: In this study, we obtained 13 nearly complete mitochondrial genomes from Late Pleistocene to early Holocene bovine samples from Northeastern China through fossil sample collection, ancient DNA extraction, library construction, and high-throughput sequencing. Based on the acquired ancient DNA data and in combination with previously published bovine data, the phylogenetic status, lineage divergence time, and population dynamics of aurochs in Northeastern China were analyzed. Results: Phylogenetic analyses and divergence time estimations suggest that the current definition of haplogroup C is overly inclusive, necessitating a refined reclassification of this haplogroup. We also estimated the population dynamics of aurochs in Northeastern China using Bayesian skyline plots found that the maternal effective population size of the aurochs increased significantly during Marine Isotope Stage 5 (MIS5), but began to decrease in the second half of MIS3 before they eventually became extinct. Conclusions: Our results provide new molecular evidence on the phylogenetic status, divergence time, and population dynamics of aurochs in Northeastern China. Full article

Snakebite is a high-priority neglected tropical disease, and a strategic goal based on four pillars has been recommended to reduce mortality and morbidity. One is empowering rural communities through citizen science, education, and engagement. In this study, an integrative approach was used to expand our knowledge of Micrurus nigrocinctus status and characterize its venom. Using citizen science data and field visits to local communities, 99 records of M. nigrocinctus distributed in Antioquia, Chocó, and Córdoba were obtained. Children, young people, and adults recognized M. nigrocinctus as the most common coral snake species in their region, and two specimens were recovered for venomic and Phylogenetic analyses. The M. nigrocinctus venom from Colombia exhibited similar chromatographic and electrophoretic profiles and biological activities and shared nearly identical protein families with Costa Rica. Commercial coral snake antivenoms also recognized and neutralized the whole venom from both countries. However, phylogenetic relationships showed greater divergence with specimens from Costa Rica. Involving communities helps prevent coral snake bites and facilitates access to rare specimens such as M. nigrocinctus, thereby enabling venom analyses, improving antivenom evaluation, and advancing toxinology research for medically significant species. Full article

Although Cervus elaphus (Linnaeus, 1758) has been well studied, the subspecific taxonomy of Cervus canadensis populations in Qinghai and Gansu, China, is still controversial, and the mitochondrial characteristics of Cervus elaphus (Linnaeus, 1758) remain incompletely understood. We assembled 89 mitogenomes of C. canadensis from five geographical populations across Qinghai and Gansu. Phylogenetic analysis confirmed that the 89 individuals are taxonomically classified as C. c. kansuensis. Nucleotide compositions showed a higher abundance of adenine and cytosine compared to guanine and thymine in both complete mitogenomes and mitochondrial PCGs. Codon usage analysis revealed a strong preference towards A-ending codons (68.04% of over-represented codons, RSCU > 1.6) in mitochondrial PCGs, with systemic avoidance of G-ending codons (53.30% of unused codons, RSCU = 0). The CAMs of 13 PCGs are reported for the first time. Furthermore, the ENC plot showed that the codon usage of all PCGs was biased except for gene ATP8. The PR2 bias plot showed that gene ND6 exhibited bias towards T3 and G3, whereas the other genes preferred A3 and C3. Both the ENC-plot and PR2 bias plot suggested that natural selection played an important role in the forces driving codon usage bias in mitochondrial PCGs. Our results demonstrate the subspecific status of C. canadensis distributed in Qinghai and Gansu as C. c. kansuensis, and provide insights into the mitochondrial characteristics of C. c. kansuensis. The mitogenome sequences assembled in this study provide valuable data for further understanding of the Cervus elaphus (Linnaeus, 1758) mitogenome. Full article

Studies on the gain or loss of nectar during the course of evolution in Dendrobium Sw. (Orchidaceae) are able to provide important information concerning the reproductive biology of this enormous orchid genus and highlight reproductive barriers—in particular, changes to compatibility. By employing a literature search on the compatibility system of Dendrobium, supplemented by new experimental data of 13 taxa investigated by means of microscopy, histochemistry, and phylogenetic analysis, we aimed to ascertain whether there is, in this genus, a relationship between self-compatibility (SC) and the presence of nectar. Nectariferous plant species are thought to be visited more frequently by pollinators, resulting in geitonogamy or selfing; therefore, the presence of nectar in some Dendrobium species may promote self-incompatibility (SI), whereas a lack of nectar may increase cross-pollination. Our investigations confirmed that the capacity for nectar secretion was gained and lost several times in this genus, and that similarly organized nectar spurs were present in all species investigated, regardless of their ability to produce nectar. SI, SC, and the presence or absence of nectar have all evolved independently, but, of the 42 taxa investigated whose status both relating to nectar presence and compatibility was known, nectar was more frequent in self-incompatible taxa. Full article