Search Results (154)

Sapindus delavayi is a drought-resistant tree species endemic to the dry–hot valleys of Southwestern China and is of great significance for soil and water conservation and ecological restoration. In this study, we sequenced the transcriptome of its leaves using the Illumina HiSeq 4000 platform and obtained 96.12 Gb of high-quality data (Q20 = 98.68%, Q30 = 95.62%), which were de novo assembled to obtain 89,228 unigenes (N50 = 1538 bp), of which 63,005 (70.61%) were successfully annotated to at least one database (NR, NT, SwissProt, KOG, KEGG, GO, Pfam). Overall, 53.96% of the unigenes in the S. delavayi leaves were annotated to Acer yangbiense, which belongs to the same family as S. delavayi. A total of 42,870 CDSs and 21,488 SSR loci were detected, with the highest mononucleotide repeat rate at 42.72% of the total number. Drought stress experiments identified 669–1203 differentially expressed genes (DEGs). Through our research, the first high-quality transcriptome database of S. delavayi has been constructed and its drought-resistance-related gene features have been analyzed, laying an important foundation for future functional gene mining, molecular marker development, molecular diversity studies, molecular breeding, and ecological adaptation research. Full article

Background/Aims: Ledrinae comprises about 460 described species across five tribes and represents an early-branching, morphologically distinctive lineage of leafhoppers, yet its intra-subfamilial relationships remain ambiguous owing to limited mitogenomic sampling. Here, we sequence and annotate the complete mitochondrial genome of Petalocephala arcuata—only the 18th Ledrinae mitogenome—to broaden taxon coverage within the genus and furnish critical molecular data for rigorously testing Ledrinae monophyly and refining tribal and genus level phylogenetic hypotheses. Methods: In this study, we sequenced and annotated the complete mitochondrial genome of P. arcuata via Illumina sequencing and de novo assembly, and reconstructed the phylogeny of 62 Cicadellidae species using maximum likelihood and Bayesian inference methods. Results: The 14,491 bp circular mitogenome of P. arcuata contains 37 genes with 77.4% A+T. All PCGs use ATN start codons except ND5 (TTG), and codon usage is A or U biased. Of 22 tRNAs, only trnS1 lacks a DHU arm, while the others adopt the canonical cloverleaf structure. Bayesian inference and maximum likelihood analyses produced broadly congruent topologies with mostly high nodal support, recovering Ledrinae as monophyletic and clustering all Petalocephala species into a well-supported clade. Conclusions: In this study, we enriched the molecular resources for the genus Petalocephala by sequencing, annotating, and analyzing the complete mitochondrial genome of P. arcuata. Phylogenetic reconstructions based on these genomic data align closely with previous morphological diagnoses, further confirming the monophyly of the genus Petalocephala. Full article

Hexagrammos otakii, also commonly called “Fat Greenling”, is highly valued as an important commercial fish due to its extremely delicious flesh. However, the absence of a genomic resource has limited our understanding of its genetic characteristics and hindered artificial breeding efforts. In this study, we performed Illumina paired-end sequencing of H. otakii, generating a total of 73.19 Gb of clean data. Based on K-mer analysis, the genome size was estimated to be 679.23 Mb, with a heterozygosity rate of 0.68% and a repeat sequence proportion of 43.60%. De novo genome assembly using SOAPdenovo2 resulted in a draft genome size of 723.31 Mb, with the longest sequence length being 86.24 Kb. Additionally, the mitochondrial genome was also assembled, which was 16,513 bp in size, with a GC content of 47.20%. Minisatellites were the most abundant tandem repeats in the H. otakii genome, followed by microsatellites. In the phylogenetic tree, H. otakii was placed within a well-supported clade (bootstrap support = 100%) that included S. sinica, N. coibor, L. crocea, and C. lucidus. PSMC analysis revealed that H. otakii underwent a population bottleneck during the Pleistocene, peaking around 500 thousand years ago (Kya) and declining to a minimum during the Last Glacial Period (~70–15 Kya), with no significant recovery observed by ~10 Kya. This study was a comprehensive genome survey analysis of H. otakii, providing insights into its genomic characteristics and population dynamics. Full article

Pholiota nameko (T. Ito) S. Ito and S. Imai is an emerging wild mushroom species belonging to the genus Pholiota. Its unique brown–yellow appearance and significant biological activity have garnered increasing attention in recent years. However, there is a relative lack of research on the biological characteristics and genetics of P. nameko, which greatly limits the potential for an in-depth exploration of this mushroom in the research fields of molecular breeding and evolutionary biology. This study aimed to address that gap by employing Illumina and Nanopore sequencing technologies to perform whole-genome sequencing, de novo assembly, and annotation analysis of the P. nameko ZZ1 strain. Utilizing bioinformatics methods, we conducted a comprehensive analysis of the genomic characteristics of this strain and successfully identified candidate genes associated with its mating type, carbohydrate-active enzymes, virulence factors, pan-genome, and drug resistance functions. The genome of P. nameko ZZ1 is 24.58 Mb in size and comprises 33 contigs, with a contig N50 of 2.11 Mb. A hylogenetic analysis further elucidated the genetic relationship between P. nameko and other Pholiota, revealing a high degree of collinearity between P. nameko and ZZ1. In our enzyme analysis, we identified 246 enzymes in the ZZ1 genome, including 68 key carbohydrate-active enzymes (CAZymes), and predicted the presence of 11 laccases, highlighting the strain’s strong potential for cellulose degradation. We conducted a pan-genomic analysis of five closely related strains of Pholiota, yielding extensive genomic information. Among these, there were 2608 core genes, accounting for 21.35% of the total genes, and 135 dispensable genes, highlighting significant genetic diversity among Pholiota and further confirming the value of pan-genomic analysis in uncovering species diversity. Notably, while we successfully identified the A-mating-type locus, composed of the homeodomain protein genes HD1 and HD2 in ZZ1, we were unable to obtain the B-mating-type locus due to technical limitations, preventing us from acquiring the pheromone receptor of the B-mating-type. We plan to supplement these data in future studies and explore the potential impact of the B-mating-type locus on the current findings. In summary, the genome data of ZZ1 presented in this study are not only valuable resources for understanding the genetic basis of this species, but also serve as a crucial foundation for subsequent genome-assisted breeding, research into cultivation technology, and the exploration of its nutritional and potential medicinal value. Full article

The Chilean oyster (Ostrea chilensis) is a flat oyster native to Chile and New Zealand. Over-exploitation has led to local extinctions in some areas. Two phenotypes, distinguished by dark or white mantle edge pigmentation, have been identified, with the dark-edged mantle oysters being more commercially valuable due to perceived quality. In this study, transcriptomic data were obtained from the mantles of both phenotypes. Total RNA was extracted of adult Chilean Oyster mantle, and samples were sequenced using HiSeq X Illumina technology. A total of 935,620,583 paired-end reads were de novo assembled, 50,908 transcripts produced, and a reference transcriptome created with 37.92% GC content and an N50 of 1929 bp. Functional annotation showed a total of 51,315 GO terms, with 21,322 annotations on Biological Process, 14,578 annotations on Molecular Functions, and 15,415 annotations on Cellular Component. The RNA-seq analysis revealed 746 differentially expressed transcripts, 573 up-regulated and 173 transcripts down-regulated, between dark- and white-mantle edge Chilean Oyster. KEGG enrichment analysis revealed notable differences in the expression profiles allowing the detection of differential expressed transcripts associated with specific pathways such as Ribosome, Citrate cycle, and Protein processing in endoplasmic reticulum. Other interesting differentially represented pathways include Tyrosine metabolism, Tryptophan metabolism, cAMP signaling pathway, ABC transporters, Notch signaling pathway, Endocytosis, and Calcium signaling pathway. This dataset provides a valuable molecular resource for O. chilensis and the understanding of the molecular mechanisms involved in mantle edge pigmentation. Full article

Lasiodiplodia theobromae is a pathogenic fungus associated with tropical perennial fruit plants worldwide. In apple trees, L. theobromae causes dieback and canker, a disease that affects the architecture of the wood producing the progressive death of branches and stems, from the tips to the base, invading the vascular tissue, manifesting necrotic lesions in the bark, impeding the flow of nutrients and water. The present work reports the whole genome de novo sequencing (WGS) of L. theobromae strain Bot-2018-LT45 isolated from apple trees with dieback symptoms. Genomic DNA of L. theobromae was sequenced using Illumina paired-end short-read technology (NovaSeq6000) and PacBio SMRTbell^TM (Single Molecule, Real-Time) long-read technology. The genome size was 44.17 Mb. Then, assembly and annotation revealed a total of 12,948 genes of which 11,634 encoded proteins. The genome was assembled into 34 contigs with an N50 (Mb) value of 3.23. This study is the first report of the L. theobromae genome de novo obtained from apple trees with dieback and canker symptoms in the Maule Region, Chile. This genetic information may set the basis for future study of the mechanisms of L. theobromae and establish the possibility of specific molecular improvements for the control of dieback and canker. Full article

Background/Objectives: Infections caused by multidrug-resistant (MDR)bacteria pose a significant public health threat by worsening patient outcomes, contributing to hospital outbreaks, and increasing health and economic burdens. Advanced genomic tools enhance the detection of resistance genes, virulence factors, and high-risk clones, thus improving the management of MDR infections. In the Autonomous Community of Aragon, the diversity and incidence of carbapenemase-producing Enterobacteriaceae (CPE) have increased during the last years. This study analyses CPE trends at a tertiary hospital in Spain from 2021 to 2023, aiming to optimize personalized medicine. Methods: CPE isolates were the first isolate per patient, year, species, and carbapenemase from January 2021 to December 2023. Additional metadata were collected from the laboratory’s information system. Antibiotic susceptibility testing was performed by broth microdilution. Whole-genome sequencing (WGS) was performed using Illumina short reads. De novo assembly was used to generate draft genomes in order to determine their complete taxonomic classification, resistome, plasmidome, sequence type (ST), core–genome multilocus sequence typing (cgMLST), and phylogenetic relationships using a suite of bioinformatics tools and in-house scripts. Results: Between 2021 and 2023, 0.4% out of 38,145 Enterobacteriaceae isolates were CPE. The CPE rate tripled in 2022 and doubled again in 2023. The most common species was Klebsiella pneumoniae (51.8%) and the most common carbapenemase was bla_OXA-48. WGS revealed concordant species identification and the carbapenemase distribution in detail. Resistance rates to critical antibiotics, such as carbapenems, were variable, but in most cases were above 70%. Genetic diversity was observed in WGS and phylogenetic analyses, with plasmids often mediating carbapenemase dissemination. Conclusions: The increasing rate of CPE in healthcare settings highlights a critical public health challenge, with limited treatment options. Genomic characterization is essential to understanding resistance mechanisms, aiding therapy, limiting outbreaks, and improving precision medicine. Full article

The green peach aphid (Myzus persicae) is a generalist pest damaging crops and transmitting viral pathogens. Using Illumina sequencing of small (s)RNAs and poly(A)-enriched long RNAs, we analyzed aphid virome components, viral gene expression and antiviral RNA interference (RNAi) responses. Myzus persicae densovirus (family Parvoviridae), a single-stranded (ss)DNA virus persisting in the aphid population, produced 22 nucleotide sRNAs from both strands of the entire genome, including 5′- and 3′-inverted terminal repeats. These sRNAs likely represent Dicer-dependent small interfering (si)RNAs, whose double-stranded RNA precursors are produced by readthrough transcription beyond poly(A) signals of the converging leftward and rightward transcription units, mapped here with Illumina reads. Additionally, the densovirus produced 26–28 nucleotide sRNAs, comprising those enriched in 5′-terminal uridine and mostly derived from readthrough transcripts and those enriched in adenosine at position 10 from their 5′-end and mostly derived from viral mRNAs. These sRNAs likely represent PIWI-interacting RNAs generated by a ping-pong mechanism. A novel ssRNA virus, reconstructed from sRNAs and classified into the family Flaviviridae, co-persisted with the densovirus and produced 22 nucleotide siRNAs from the entire genome. Aphids fed on plants versus artificial diets exhibited distinct RNAi responses affecting densovirus transcription and flavivirus subgenomic RNA production. In aphids vectoring turnip yellows virus (family Solemoviridae), a complete virus genome was reconstituted from 21, 22 and 24 nucleotide viral siRNAs likely acquired with plant phloem sap. Collectively, deep-sequencing analysis allowed for the identification and de novo reconstruction of M. persicae virome components and uncovered RNAi mechanisms regulating viral gene expression and replication. Full article

Background/Objectives: Sium serra is distributed in Korea, China, and Japan. It was first identified as the genus Pimpinella and then reclassified as Sium by Kitagawa. Some Sium species are used as herbal medicine and are often confused with the similar form Ligusticum sinense. In this study, we analyzed the cp genome of S. serra and conducted comparative analyses with the cp genomes of related taxa. Methods: We extracted gDNA from fresh leaves and sequenced it using Illumina HiSeq2500. For the chloroplast genome assembly, de novo assembly was performed using Velvet v1.2.07. For the annotation, GeSeq and NCBI BLASTN were used. Afterwards, related taxa were analyzed using programs such as DnaSP and MISA. Results: S. serra was excluded from the study on the chloroplast (cp) genome in Sium because it was classified as Pimpinella in China. Therefore, this study aimed to analyze the cp genome of S. serra for the first time and its location within the genus Sium. The complete cp genome of S. serra was 154,755 bp in length, including a pair of inverted repeats, each 26,255 bp, a large single-copy region of 84,581 bp, and a small single-copy region of 17,664 bp. The cp genome comprised 79 protein-coding, 30 tRNA, and 4 rRNA genes. Furthermore, six regions of high nucleotide diversity were identified in the genus Sium. In the genus Sium, 1630 repeats that can serve as markers were also identified. Eight protein-coding genes with high K_A/K_S values were under positive selection in the Sium. Our phylogenetic analyses suggest that S. serra was positioned with high bootstrap support within the Sium of the tribe Oenantheae, specifically in the southern Palearctic subclade. Conclusions: In this study, the S. serra chloroplast genome was sequenced and assembled. The genus Sium formed a monophyletic group; however, as not all the Sium species were included in this study, further research is necessary. This study can serve as foundational data not only for Sium but also for the tribe Oenantheae. Full article

Agave is a significant fiber crop in tropical regions, known for its high fiber strength. Lignin is closely associated with fiber strength, and phenylalanine ammonia-lyase (PAL) serves as the initial enzyme in biosynthesis of lignin. Hence, it is of considerable significance to study the genes of PAL family to analyze the characteristics and mechanism of sisal fiber development. In this research, we conducted a transcriptomic analysis of Agave schidigera, a widely recognized ornamental plant in agave. Approximately 29.85 million clean reads were acquired through Illumina sequencing. In total, 116,602 transcripts including 72,160 unigenes were assembled, and 22.06~63.56% of those unigenes were annotated in public databases. Two, six, six and six PAL genes were successfully identified and cloned from A. schidigera, A. deserti, A. tequilana and A. H11648, respectively. After phylogenetic analysis, these genes were clustered into two branches. Genes AhPLA2a and AhPLA2c exhibited higher expression levels compared to other genes but had different expression patterns. Moreover, AhPLA2a and AhPLA2c were expressed at high levels under full-nutrient, nitrogen-free and phosphorus-free stresses. Most PAL genes were induced by Phytophthora nicotianae Breda, especially AhPAL1a, AhPAL1b, AhPAL2b and AhPAL2c. This research is the first work to present a de novo transcriptome dataset for A. schidigera, enriching its bioinformation of transcripts. The cloned PAL genes and the expression analyses will form the basis of future research on lignin biosynthesis, the relationship between lignin and fiber strength, and stress resistance in Agave species. Full article

Gaillardia pulchella is an important plant species with pharmacological and ornamental applications. It contains a wide array of phytocompounds which play roles against diseases. In vitro propagation requires callogenesis and differentiation of plant organs, which offers a sustainable, alternative synthesis of compounds. The morphogenetic processes and the underlying mechanisms are, however, known to be under genetic regulation and are little understood. The present study investigated these events by generating transcriptome data, with de novo assembly of sequences to describe shoot morphogenesis molecularly in G. pulchella. The RNA was extracted from the callus of pre- and post-shoot organogenesis time. The callus induction was optimal using leaf segments cultured onto MS medium containing α-naphthalene acetic acid (NAA; 2.0 mg/L) and 6-benzylaminopurine (BAP; 0.5 mg/L) and further exhibited a high shoot regeneration/caulogenesis ability. A total of 68,366 coding sequences were obtained using Illumina150bpPE sequencing and transcriptome assembly. Differences in gene expression patterns were noted in the studied samples, showing opposite morphogenetic responses. Out of 10,108 genes, 5374 (53%) were downregulated, and there were 4734 upregulated genes, representing 47% of the total genes. Through the heatmap, the top 100 up- and downregulating genes’ names were identified and presented. The up- and downregulated genes were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Important pathways, operative during G. pulchella shoot organogenesis, were signal transduction (13.55%), carbohydrate metabolism (8.68%), amino acid metabolism (5.11%), lipid metabolism (3.75%), and energy metabolism (3.39%). The synthesized proteins displayed phosphorylation, defense response, translation, regulation of DNA-templated transcription, carbohydrate metabolic processes, and methylation activities. The genes’ product also exhibited ATP binding, DNA binding, metal ion binding, protein serine/threonine kinase -, ATP hydrolysis activity, RNA binding, protein kinase, heme and GTP binding, and DNA binding transcription factor activity. The most abundant proteins were located in the membrane, nucleus, cytoplasm, ribosome, ribonucleoprotein complex, chloroplast, endoplasmic reticulum membrane, mitochondrion, nucleosome, Golgi membrane, and other organellar membranes. These findings provide information for the concept of molecular triggers, regulating programming, differentiation and reprogramming of cells, and their uses. Full article

Hereditary thoracic aorta diseases (HTADs) are a heterogeneous group of rare disorders whose major manifestation is represented by aneurysm and/or dissection frequently located at the level of the ascending thoracic aorta. The diseases have an insidious evolution and can be encountered as an isolated manifestation or can also be associated with systemic, extra-aortic manifestations (syndromic HTADs). Along with the development of molecular testing technologies, important progress has been made in deciphering the heterogeneous etiology of HTADs. The aim of this study is to identify the genetic variants associated with a group of patients who presented clinical signs suggestive of a syndromic form of HTAD. Genetic testing based on next-generation sequencing (NGS) technology was performed using a gene panel (Illumina TruSight Cardio Sequencing Panel) or whole exome sequencing (WES). In the majority of cases (8/10), de novo mutations in the FBN1 gene were detected and correlated with the Marfan syndrome phenotype. In another case, a known mutation in the TGFBR2 gene associated with Loeys–Dietz syndrome was detected. Two other pathogenic heterozygous variants (one de novo and the other a known mutation) in the SLC2A10 gene (compound heterozygous genotype) were identified in a patient diagnosed with arterial tortuosity syndrome (ATORS). We presented the genotype–phenotype correlations, especially related to the clinical evolution, highlighting the particularities of each patient in a family context. We also emphasized the importance of genetic testing and patient monitoring to avoid acute aortic events. Full article

Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata, and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure. Methods: Samples were collected for mitogenome assembly (n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo, and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes. Results: The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φ_ST (0.047). Conclusions: Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units. Full article

The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species. Full article

Background: Wiedemann–Steiner syndrome (WSS), a rare autosomal-dominant disorder caused by haploinsufficiency of the KMT2A gene product, is part of a group of disorders called chromatinopathies. Chromatinopathies are neurodevelopmental disorders caused by mutations affecting the proteins responsible for chromatin remodeling and transcriptional regulation. The resulting gene expression dysregulation mediates the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disorders. Aim of the Study: The aim of this study was to investigate a 10-year-old girl who presented with clinical features suggestive of WSS. Methods: Clinical and genetic investigations were performed. Whole exome sequencing (WES) was used for genetic testing, performed using Illumina technology. The bidirectional capillary Sanger resequencing technique was used in accordance with standard methodology to validate a mutation discovered by WES in all family members who were available. Utilizing computational protein modeling for structural and functional studies as well as in silico pathogenicity prediction models, the effect of the mutation was examined. Results: WES identified a de novo heterozygous missense variant in the KMT2A gene KMT2A(NM_001197104.2): c.3451C>G, p.(Arg1151Gly), absent in the gnomAD database. The variant was classified as Likely Pathogenetic (LP) according to the ACMG criteria and was predicted to affect the CXXC-type zinc finger domain functionality of the protein. Modeling of the resulting protein structure suggested that this variant changes the protein flexibility due to a variation in the Gibbs free energy and in the vibrational entropy energy difference between the wild-type and mutated domain, resulting in an alteration of the DNA binding affinity. Conclusions: A novel and de novo mutation discovered by the NGS approach, enhancing the mutation spectrum in the KMT2A gene, was characterized and associated with WSS. This novel KMT2A gene variant is suggested to modify the CXXC-type zinc finger domain functionality by affecting protein flexibility and DNA binding. Full article