Search Results (2,090)

A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2^T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2^T represents a distinct species within the genus, clearly separated from its closest relatives, namely Methylocystis suflitae NLS-7^T, Methylocystis rosea SV97^T, Methylocystis silviterrae FS^T, and Methylocystis hirsuta CSC1^T. As is typical of the family Methylocystaceae, cells possess intracytoplasmic membranes arranged parallel to the cytoplasmic membrane, and the dominant fatty acids are C18:1ω8c and C18:1ω7c. The strain grows aerobically on methane as the primary carbon and energy source and expresses both low- and high-affinity particulate methane monooxygenase (pMMO), but lacks the soluble form. The species epithet reflects the strain’s ability to utilize hydrogen as an alternative energy source. A further feature is its use of asparagine as an osmoprotectant, enhancing salt tolerance. Genomic analysis reveals complete pathways for nitrogen fixation, denitrification, and hydrogen oxidation. These genetic and physiological characteristics support the designation of a novel species, for which the name Methylocystis hydrogenophila sp. nov. is proposed. The type strain is SC2^T (=DSM 114506 = NCIMB 15437). Full article

The microhylid frog Microhyla fissipes is a protected terrestrial wildlife species in China, recognized for its ecological, economic, and scientific value. However, its mitochondrial genome remains poorly characterized. To address this gap, we sequenced and annotated the complete mitogenome of M. fissipes to elucidate its structural organization and phylogenetic placement within Microhylidae. The assembled mitogenome is 16,723 bp in length and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, and 22 tRNAs, along with one control region and the origin of heavy-strand replication. We also identified eight overlapping regions and eleven intergenic spacers. The overall base composition showed an A + T bias (59.91%) with negative AT-skew (−0.04) and GC-skew (−0.27). All tRNAs displayed typical cloverleaf secondary structures, except for trnS1, which lacked the D-arm. Phylogenetic reconstruction using both maximum likelihood and Bayesian inference strongly supported the monophyly of Microhylidae and revealed a sister-group relationship between Microhyla and Kaloula. Within Microhyla, M. fissipes was most closely related to M. heymonsi, with which it formed a well-supported clade that also included Microhyla okinavensis, Microhyla mixtura, and Microhyla beilunensis. Selection pressure analysis on protein-coding genes indicated widespread purifying selection (Ka/Ks < 1) across most genes, except for ATP8, COX2, and COX3, which may be under relaxed selective constraints. These findings offer valuable genomic resources for the conservation of M. fissipes and provide new insights into the phylogeny and evolution of microhylid frogs. Full article

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development. Full article

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding. Full article

Soft-furred tree mice (genus Typhlomys), which are native to southern China and northern Vietnam, are unique rodents capable of echolocation. Little is known about their taxonomy, ecology, and natural history. In this study, we generated the complete mitochondrial genomes of seven species/putative species of Typhlomys. We conducted a comprehensive comparative analysis of these mitochondrial genomes focusing on sequence length, A+T content, A/T bias, A+T-rich regions, overlapping and intergenic spacer regions, nucleotide composition, relative synonymous codon usage, ancestral distributions, and the non-synonymous/synonymous substitution ratio (Ka/Ks). Additionally, we analyzed the phylogeny and adaptive evolution of these species/putative species. The mitogenomes of Typhlomys ranged from 16,487 to 17,380 bp in length, encoding the complete set of 37 genes typically found in mammalian mitogenomes. The base composition exhibited an A+T bias. The most frequently used codons were CUA (Leu), AGC (Ser), GGA (Gly) and UUA (Leu), UUG, CUG, CGU and GCG were the less frequently used codons. Ancestral distribution reconstruction suggests that Typhlomys originated in Central or Southwestern China. Notably, we found that the Ka/Ks ratio of the ND5 gene in T. huangshanensis was greater than 1, indicating that this gene has undergone positive selection for efficient respiration in higher elevations and colder climates. Full article

Bacillus cereus sensu lato is widespread and causes significant food spoilage that alters the flavour and structure of milk. The present study investigated the prevalence, enterotoxigenic genes, and resistant profiles of B. cereus strains isolated from raw milk of Bos taurus in South Africa (the Eastern Cape Province). One thousand four hundred samples were obtained from commercial dairy farms and were evaluated for the presence of B. cereus using B. cereus selective agar, and genomic DNA was isolated from B. cereus colonies with specific characteristics. PCR was used to evaluate the presence of enterotoxigenic genes, and antibacterial susceptibility was carried out using the Kirby-Bauer Disc diffusion method. The result revealed that B. cereus was detected in 250 raw milk samples. In addition, 67.2% of the isolates grew when incubated at 4 °C. Among the enterotoxigenic genes studied, ces showed the highest occurrence (88.8%), but hblABC (0%) did not demonstrate amplification from any isolate. Our analysis found two significant patterns (III and V): nheABC-entFM (27.2% and 24.4%) and the ces gene. Total (100%) sensitivity was observed for six of the twelve antibiotics tested, while organisms showed complete resistance to penicillin and rifampicin. This study marks the initial documentation of B. cereus and its enterotoxigenic genes in Bos taurus raw milk sourced from the Eastern Cape Province, South Africa. Enterotoxin FM should be considered the second most crucial enterotoxin, after non-hemolytic enterotoxin, and should be included in the molecular approach used to classify pathogenic B. cereus in nutrimental products. These findings underscore the urgent need for public health awareness, particularly in rural communities where raw milk consumption is prevalent. The high prevalence of antibiotic resistance and toxigenic strains of B. cereus calls for improved milk pasteurization practices to mitigate the risk of foodborne illness. Full article

The Flaviviruses Dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), and Yellow Fever virus (YFV), are mosquito-borne viruses that represent a persistent challenge to global health due to the emergence and re-emergence of outbreaks of significant magnitudes. Their positive-sense RNA genome, about 11,000 nucleotides long, encodes structural and nonstructural proteins. These viruses evolve rapidly through mutations and genetic recombination, which can lead to more virulent and transmissible strains. Although whole-genome sequencing is ideal for studying their evolution and geographic spread, its cost is a limitation. We investigated the genetic variability of DENV, ZIKV, WNV, and YFV to identify genomic regions that accurately reflect the phylogeny of the complete coding sequence and evaluated the utility of these regions in reconstructing the geographic dispersal patterns of viral genotypes and lineages. Publicly available sequences from GenBank were examined to assess variability, reconstruct phylogenies, and identify the most informative genomic regions. Once representative regions were identified, they were used to infer the global phylogeographic structure of each virus. The virus depicted distinct variation patterns, but conserved regions of high and low variability were common to all. Highly variable regions of ~2700 nt offered greater resolution in phylogenetic trees, improving the definition of internal branches and statistical support for nodes. In some cases, combined multiple highly variable regions enhanced phylogenetic accuracy. Phylogeographic reconstruction consistently grouped sequences by genotype and geographic origin, with temporal structuring revealing evolutionarily distinct clusters that diverged over decades. These findings highlight the value of targeting genomic regions for phylogenetic and phylogeographic analysis, providing an efficient alternative for genomic surveillance. Full article

As nutrient allocation trade-offs occur between reproductive and vegetative development in crops, optimizing their partitioning holds promise for improving agricultural productivity and quality. Herein, we characterize the phenotypic diversity of the fruitfulness trait and identify associated genes in tea plants (Camellia sinensis). Over three consecutive years, we monitored the fruitfulness of an F₁ hybrid population (n = 206) derived from crosses of ‘Emei Wenchun’ and ‘Chuanmu 217’. A marked variation was observed in the yield of individual plants, ranging from complete sterility (zero fruits) to exceptionally high fertility (1612 fruits). Using the high-resolution genetic linkage map and the fruitfulness data, we identified a stable major QTL designated as qFN5. To fine-map the underlying gene(s), artificial pollination experiments were conducted with extreme phenotype individuals (with the highest vs. lowest fruit numbers). Bulked segregant RNA sequencing (BSR-Seq) with ovules collected at two and seven days post-pollination (DPP) identified the genomic intervals that exhibit a high degree of overlap with qFN5. Analysis of expression dynamics combined with functional genomics data revealed a prominent candidate gene, CsETR2 (TGY048509), which encodes an ethylene receptor protein. When CsETR2 was overexpressed in Arabidopsis thaliana, the transgenic lines exhibited significantly decreased reproductive performance relative to the wild-type plants. Relative to the wild type, the transgenic lines exhibited a significant decline in several key traits: the number of effective panicles decreased by 72.5%, the seed setting rate dropped by 67.7%, and the silique length shortened by 38%. These findings demonstrate its role in regulating plant fruitfulness. Furthermore, yeast one-hybrid and dual-luciferase assays verified that CsMYB15 (TGY110225) directly binds to the CsETR2 promoter, thus repressing its transcription. In summary, our findings expand the understanding of genetic regulation underlying fruitfulness in tea plants and provide candidate target loci for breeding. Full article

In recent years, symptoms suggestive of viral infection have commonly occurred in Gynura bicolor in China. However, no viral genome infecting G. bicolor has been reported. This study applied high-throughput sequencing to plant samples with chlorotic spots in Sanya, Hainan. Viral sequences were confirmed using RT-PCR and RACE. Complete genomes of vanilla distortion mosaic virus (VDMV, Potyvirus vanillae) and an unknown virus were obtained. Sequence analysis indicated that the VDMV isolate from the G. bicolor is a novel variant. It shares 81.13% identity with its closest known strain. The unknown virus is phylogenetically related to maculaviruses but shares less than 76% nucleotide identity with other tymovirids. According to the ICTV, it should be classified as a new member of the genus Maculavirus. In this study, we provisionally designated the virus as gynura bicolor maculavirus (GBMV). Transmission electron microscopy revealed both filamentous and icosahedral virions in stems, but only filamentous virions in leaves. Quantitative RT-PCR showed high RNA accumulation of both viruses in the stems. GBMV levels were significantly lower in leaves. Dodder-mediated mechanical transmission successfully transferred VDMV and GBMV to Nicotiana occidentalis, Oenothera biennis, and Chenopodium amaranticolor. O. biennis developed chlorotic symptoms 15 days after dual infection. Full article

Background: Grewia is a genus of flowering plants belonging to the Malvaceae family. Grewia tembensis is used in traditional medicine for the treatment of several microbial diseases as well as a livestock feed. Methods: In the current study, the complete chloroplast (cp) genome of G. tembensis was constructed using data derived from high-throughput sequencing, followed by comprehensive analyses and comparison with phylogenetically related species. Results: The chloroplast genome of G. tembensis is 158,040 bp long and has the typical quadripartite structure found in angiosperms. The large single-copy (LSC) segment measures 86,956 bp, whereas the small single-copy (SSC) regions encompass 20,142 bp. The two inverted repeat (IRa and IRb) regions have an identical length of 25,471 bp and display a higher degree of conservation relative to the single-copy (SC) regions based on nucleotide diversity analysis. The genome of G. tembensis possesses 130 genes. The simple sequence repeat (SSR) numbers ranged between 202 and 234 repeats in Grewioideae subfamily species under this study. Furthermore, nucleotide diversity analysis demonstrated a marked elevation in polymorphism information (Pi) values across 30 genes in Grewioideae. Conclusions: cpSSRs can be used for the examination of population genetic variability within and between Grewia species, as well as the categorization of populations and their biogeographical distribution. In addition, loci with high Pi values can contribute substantial genetic variability, which is crucial for addressing taxonomic dilemmas in phylogenetic investigations. Full article

Duck viral hepatitis, caused by Duck Hepatitis A Virus Type 3 (DHAV-3), remains a major threat to young ducklings. Although DHAV-3 has circulated in China since the 1999s, the complete genomic architecture, exact virulence parameters, and evolutionary distance between early Yunnan isolates and current field strains have remained undefined. This study investigated six DHAV-3 strains isolated in Yunnan Province, China, between 2004 and 2006, to elucidate their genetic and biological characteristics. Full-genome sequencing and phylogenetic analysis revealed >99.5% nucleotide and >99.6% amino acid identity among the strains, suggesting a common ancestral origin. In vivo challenge assays showed rapid onset of clinical signs and >90% mortality in ducklings within 36 h post-inoculation. Embryonic deaths began at 24 h post-infection and peaked by 90 h. Viral replication was efficient in DEF, DEK, Vero, and BHK-21 cells, but absent in chicken fibroblasts (DF-1). Comparative genomic analysis between the YN/LR/2005 strain and recent field isolates (2022–2024) revealed substantial nucleotide divergence in structural regions, with 32 unique amino acid substitutions—all five located in the immunodominant VP1 region that may influence viral antigenicity and host interaction—alongside changes in N-glycosylation sites and alterations in protein secondary structure. Histopathological examination confirmed characteristic hepatic lesions. These findings demonstrate that while DHAV-3 has undergone genetic evolution, it retains high virulence, underscoring the need for ongoing molecular surveillance and supporting future vaccine and diagnostic development. Full article

Colorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and long-read Nanopore sequencing technologies across multiple CRC sample groups, encompassing diverse tissue morphologies. Our evaluation included general base-level metrics—such as nucleotide ratios, sequence match rates, and coverage—as well as variant calling performance, including variant allele frequency (VAF) distributions and pathogenic mutation detection rates. Focusing on clinically relevant genes (KRAS, BRAF, TP53, APC, PIK3CA, and others), we characterized platform-specific detection profiles and completed the ground truth validation of somatic KRAS and BRAF mutations. Structural variant (SV) analysis revealed Nanopore’s enhanced ability to resolve large and complex rearrangements, with consistently high precision across SV types, though recall varied by variant class and size. To enable direct comparison with the Illumina exome panel, we applied an exonic position reference file. To assess the impact of depth and PCR amplification, we completed an additional high-coverage Nanopore sequencing run. This analysis confirmed that PCR-free protocols preserve methylation signals more accurately, reinforcing Nanopore’s utility for integrated genomic and epigenomic profiling. Together, these findings underscore the complementary strengths of short- and long-read sequencing platforms in high-resolution cancer genomics, and we highlight the importance of coverage normalization, epigenetic fidelity, and rigorous benchmarking in variant discovery. Full article

Background/Objectives: This study aimed to profile the molecular variants of muscle-invasive bladder cancer (MIBC) based on immunohistochemical analysis and to make a correlation with morphological characteristics in a series of 100 consecutive patients. Methods: A retrospective single-center study was conducted on 100 consecutive cases of MIBC (2021–2024). A selected immunohistochemical (IHC) panel (including CK5/6, CK20, and p16) was applied in all cases to classify the tumors into known molecular variants (luminal papillary, luminal non-specified, luminal unstable, stroma-rich, basal/squamous, neuroendocrine-like). Results: Seven molecular subtypes are identified: basal (33%), luminal papillary (24%), luminal unstable (16%), luminal non-specified (10%), basoluminal (double-positive) (9%), neuroendocrine-like (double-negative with neuroendocrine morphology) (6%), and stroma-rich (2%). This distribution largely matches published data (Consensus Classification and The Cancer Genome Atlas (TCGA)), with minor differences (e.g., a lower share of the stroma-rich variant). A strong correlation is found between the histological subtypes of some tumors and their molecular variant (χ², p < 0.001): for example, all cases of urothelial carcinoma with squamous differentiation are basal, micropapillary tumors are entirely luminal, and small-cell carcinomas are neuroendocrine-like. Conclusions: The results demonstrate that the morphological subtype of urothelial carcinoma largely predetermines the molecular profile. Combining classic histopathology with IHC-based profiling allows for a more complete characterization of the tumor and aids prognosis and personalized treatment in MIBC. Full article

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (O_L), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article

Eryngium foetidum L. belongs to the Apiaceae family and is a perennial herb. The entire plant is rich in essential oils, which have a distinctive aroma similar to cilantro. This plant exhibits significant biological activity and possesses characteristics such as disease resistance and antimicrobial properties, showing great potential in medical and food applications. Additionally, its essential oil has substantial commercial value. Mitochondria play a crucial role as organelles within plant cells; however, the mitochondrial genome of E. foetidum remains underexplored. To fill this research gap, we conducted sequencing and assembly of the mitochondrial genome of E. foetidum, aiming to uncover its genetic mechanisms and evolutionary trajectories. Our investigation reveals that the mitochondrial genome of E. foetidum is a circular structure, similar to that of other species, with a length of 241,660 bp and a GC content of 45.35%, which is within the range observed in other organisms. This genome encodes 59 genes, comprising 37 protein-coding sequences, 18 tRNA genes, and 4 rRNA genes. Comparative analysis highlighted 16 homologous regions between the mitochondrial and chloroplast genomes, with the longest segment spanning 992 bp. By analyzing 37 protein-coding genes (PCGs), we identified 479 potential RNA editing sites, which induce the formation of stop codons in the nad3 and atp6 genes, as well as start codons in the ccmFC, atp8, nad4L, cox2, cox1, and nad7 genes. Meanwhile, the genome shows a preference for A/T bases and A/T-ending codons, with 32 codons having a relative synonymous codon usage (RSCU) value greater than 1. The codon usage bias is relatively weak and mainly influenced by natural selection. Most PCGs are under purifying selection (Ka/Ks < 1), while only a few genes, such as rps7 and matR, may be under positive selection. Phylogenetic analysis of mitochondrial PCGs from 21 species showed E. foetidum at the basal node of Apiaceae, consistent with the latest APG angiosperm classification and chloroplast genome-based phylogenetic relationships. In summary, our comprehensive characterization of the E. foetidum mitochondrial genome not only provides novel insights into its evolutionary history and genetic regulation but also establishes a critical genomic resource for future molecular breeding efforts targeting mitochondrial-associated traits in this economically important species. Full article