搜索结果：DNA research : an international journal for rapid publication of reports on genes and genomes

Bats are known reservoirs for many viruses of zoonotic potential and can tolerate or clear infections efficiently. They are important hosts for multiple coronaviruses and harbour ancestral lineages of coronaviruses known to cause diseases in both humans and animals. In this study, we describe a high-quality hybrid genome assembly of the Blyth's horseshoe bat Rhinolophus lepidus. It is a widespread species and an important cell-line model system for studying virus entry and replication. We used a combination of short Illumina reads and long reads from Oxford Nanopore to assemble the genome, with N50 of 5.3 Mb and Benchmarking Universial Single-Copy Orthologs (BUSCO) score of ~94%. The Angiotensin-converting enzyme 2 receptor responsible for the entry of severe acute respiratory syndrome coronaviruses (SARS and SARS-CoV-2) was highly conserved within bats, especially the region responsible for virus entry into the cell. In total, 50% of the amino acids necessary for virus entry were conserved between humans and R. lepidus. We observed an effect of past climatic conditions on the effective population size with drastic population size reduction in the past 50,000 years. This study adds to the growing list of bat genomes which are important resources to understand the co-evolution of bats and viruses and the mechanism by which bats can tolerate and clear infections effectively.

Pontederia cordata L. is an aquatic ornamental plant native to the Americas but has been widely distributed in South Asia, Australia, and Europe. The genetic mechanisms behind its rapid adaptation and spread have not yet been well understood. To understand the mechanisms for its rapid adaptation, this study assembled the first chromosome-level genome of P. cordata. The genome assembly, which spans 527.5 Mb, is anchored on 8 pseudochromosomes with a scaffold N50 of 48 Mb and encompasses 29,389 protein-coding genes. Further analyses revealed that P. cordata had experienced 3 whole-genome duplications (WGDs) events. These WGDs are associated with gene family expansion and increased numbers of resistance gene analogs and transcription factors. Positive selection analysis indicated that genes derived from tandem duplication (TD) and proximal duplication were more likely to undergo positive selection, and were enriched in plant defense and disease resistance. These results implied that WGDs, TD, and positive selection enhanced the environmental adaptability of P. cordata. In addition, we found that down-regulation of F3'5'H, DFR, ANS, and UFGT likely caused the flower colour variation for P. cordata from violet to white. The first chromosome-level genome of P. cordata here provides a valuable genomic resource for investigating the rapid adaptation and flower colour variation of the species.

Oil palm (Elaeis guineensis Jacq.) is a globally important crop, and its genetic improvements benefit from comprehensive genome sequencing. Here, we report the whole-genome sequencing and annotation of two key genetic resources: the wild (Eg-DCM) and ancestral (Eg-DBG) Dura accessions, using a combination of short- and long-read sequencing technologies. De novo assembly followed by polishing, proximity ligation, and reference-guided scaffolding yielded high-quality assemblies with ungapped lengths of 1.71 Gb (Eg-DBG) and 1.48 Gb (Eg-DCM). Eg-DCM and Eg-DBG genomes exhibited high completeness, with over 97% of Benchmarking Universal Single-Copy Orthologs (BUSCOs) recovered across the Eukaryota, Viridiplantae, and Embryophyta datasets. Repetitive elements, particularly retrotransposons, dominated both genomes, accounting for 46.10% of Eg-DBG and 43.85% of Eg-DCM. Gene prediction initially identified 61,256 (Eg-DBG) and 53,985 (Eg-DCM) genes, which were refined into high-confidence gene sets of 39,263 and 35,298, respectively. Additionally, 1,760 and 1,684 putative resistance (R) genes were identified in Eg-DCM and Eg-DBG, with similar class distributions. The five major R gene classes comprise KIN, RLK, RLP, CNL, and CK. With further research, the assembled whole-genome sequences and the annotated genes of Eg-DBG and Eg-DCM offer valuable insights into the untapped genomic information of undomesticated accessions, with implications for future breeding and crop improvement efforts of oil palm.

Fusion genes play crucial roles in plant biological processes but remain far less explored than their human counterparts, largely due to limited validated datasets and the absence of plant-specific prediction tools. Existing approaches often produce high false-positive rates, restricting reliable discovery. To address this gap, we developed Plant Fusion Gene Predictor (PFGPred). This ensemble machine learning framework integrates Random Forest, XGBoost, and long short-term memory (LSTM) models into a meta-classifier for accurate identification of true and false fusion genes from RNA sequencing (RNA-Seq) data. PFGPred was trained on a high-confidence dataset of fusion genes validated by both RNA-Seq and whole-genome sequencing from Arabidopsis thaliana, Oryza sativa, Triticum aestivum, and Zea mays, to predict and rank candidate fusion genes for future functional validation. It outperformed individual baseline models, achieving accuracies of 0.97 on training data and 0.77 on independent test data. When evaluated on human datasets, it achieved 0.71 accuracy at the cost of lower sensitivity, reflecting biological differences between plant and human fusion events. Comparative analyses confirmed that PFGPred reliably identifies validated fusions, demonstrating its utility as a cost-effective, plant-specific prediction tool for high-throughput fusion gene screening and functional genomics research. It is freely available as a web server at http://www.nipgr.ac.in/PFGPred.

The diatom Pleurosigma pacificum is a newly described tropical pelagic species from the Western Pacific Ocean with one of largest genome size among published diatom genomes, making it an ideal candidate for studying adaptation to tropical open ocean environments and diatom evolution. We employed HiFi long-read sequencing to construct a high-quality and contaminant-free genome. The assembled genome is 1.357 Gb in size and consists of 821 contigs with a contig N50 of 3.23 Mb. The GC content is 38.6%, which is much lower than that of other published diatom genomes. The genome contains 27,408 predicted genes, 540 of which were implicated in environmental adaptation. Gene features and gene family comparisons suggest that the primary driver of genome expansion and functional diversification is long terminal repeats (LTR) retrotransposons and tandem duplications. The phylogenetic analysis revealed that the clade of P. pacificum is closely associated with other members of Naviculales. The expansion of chlorophyll a/c proteins might facilitate the adaptation of P. pacificum to high-light conditions in pelagic environments. The percentage of approximately 3.2% horizontal gene transfer (HGT) events is observed in the P. pacificum genome. HGTs are a prevalent phenomenon in diatoms and serve as a common mechanism to enhance their adaptive capabilities. In conclusion, the P. pacificum genome provides important understanding into the development of large genome size and evolutionary adaptations of pelagic diatoms.

Satellite DNAs (satDNAs) are abundant components of eukaryotic genomes, playing pivotal roles in chromosomal organization, genome stability, and evolution. Here, we combined cytogenetic and genomic methods to characterize the satDNAs in the genomes of Leptidea butterflies. Leptidea is characterized by the presence of a high heterochromatin content, large genomes, and extensive chromosomal reshuffling as well as the occurrence of cryptic species. We show that, in contrast to other Lepidoptera, satDNAs constitute a considerable proportion of Leptidea genomes, ranging between 4.11% and 11.05%. This amplification of satDNAs, together with the hyperactivity of transposable elements, contributes to the substantial genome expansion in Leptidea. Using chromosomal mapping, we show that, particularly LepSat01-100 and LepSat03-167 satDNAs, are preferentially localized in heterochromatin exhibiting variable distribution that may have contributed to the highly diverse karyotypes within the genus. The satDNAs also exhibit W-chromosome accumulation, suggesting their involvement in sex chromosome evolution. Our results provide insights into the dynamics of satDNAs in Lepidoptera genomes and highlight their role in genome expansion and chromosomal organization, which could influence the speciation process. The high proportion of repetitive DNAs in the genomes of Leptidea underscores the complex evolutionary dynamics revealing the interplay between repetitive DNAs and genomic architecture in the genus.

Several species of toxic butterflies are known, including those from the Troidini tribe of the Papilionidae, which accumulate aristolochic acid from their host plants in Aristolochiae. However, the molecular mechanisms involved in utilizing aristolochic acid remain unknown. Toxic butterflies often exhibit warning colouration to signal their toxicity to predators, a complex adaptive trait with toxin utilization. In this study, we sequenced, assembled, and annotated the genomes of 2 toxic Troidini butterflies, Pachliopta aristolochiae (312.1 Mb, 13,497 genes) and Byasa alcinous (257.6 Mb, 14,669 genes), and conducted comparative genomics to identify genes involved in toxin utilization and warning colouration. Comparative analysis across 11 species revealed 31 gene families significantly expanded and 417 genes under positive selection. Additionally, 442 genes were highly expressed in the red spots on the hindwings of P. aristolochiae. The genes shared within these lists may be involved in the formation of the complex adaptive traits of toxin utilization and warning colouration. Functional analysis using RNAi confirmed the involvement of ebony, laccase2, and tyrosine hydroxylase (TH) in warning colouration. This research marks a significant starting point in understanding the genetic basis of aristolochic acid utilization and the formation of warning colouration, providing the first list of candidate genes.

Bats (Chiroptera) are a taxonomic group of immense biological and ecological importance. They are primary reservoirs and carriers of various zoonotic viruses. Endogenous retroviruses (ERVs) originate from ancient retroviruses invading the host, and ERV-derived sequences can function as regulatory elements which influence gene expression and contribute to both physiological and pathological processes. However, ERVs and ERV-like elements (ERVLEs) carried by bats have not been fully characterized. In this study, we systematically explored the ERVs in 61 bat species and identified 10,352 bat-ERVs and 5,884 bat-ERVLEs sequences, and these sequences covered 3 major virus genera and included 7 groups related to human ERVs in the subfamily Orthoretrovirinae. In particular, a relatively intact endogenous deltaretrovirus sequence was identified in Molossus molossus. Additionally, 358 bat-ERV and 33 bat-ERVLE were identified as recombinants. The integration time of bat-ERVs was estimated to be concentrated in the last 10 to 40 million years, indicating their role in shaping the bat genome during the long-term co-evolution of virus and host. Furthermore, carnivorous bats tended to have more relatively complete and younger ERVs compared to herbivorous bats. According to bat transcriptomes, we found that 1,385 bat-ERVs and 197 bat-ERVLEs had transcriptional potential in 20 different tissues of 25 bats, implying that bat-ERVs harboured actively expressed genes with potential functions. In summary, we comprehensively characterized bat-ERVs in terms of their evolution, types and potential functions, providing foundational data and a new perspective for further research on bat-ERVs.

The giant triton snail (Charonia tritonis) is an ecologically critical predator that controls coral reef ecosystems by preying on crown-of-thorns starfish (COTS). However, overharvesting has driven severe population declines, threatening reef health. Despite its importance, the genomic underpinnings of its unique adaptations-including toxin resistance, prey detection, and environmental resilience-remain poorly understood. Here, we present the first chromosome-level genome assembly of C. tritonis (3.8 Gb), the largest sequenced gastropod genome, which encapsulates the large repetitive sequences comprising 70.1% of the genome and fueling massive genomic expansion. Macrosynteny and molecular dating analysis confirm a Jurassic-era (∼190 Mya) whole-genome duplication (WGD) that facilitated adaptive innovation. Comparative analyses identified gene family expansions critical to C. tritonis' ecological dominance: (i) toxin resistance via immune/detoxification systems (eg, galectins, Toll-like receptors, CYP450 enzymes); (ii) Sensory specialization (eg, rhodopsin expansions) enhancing prey detection in complex reef habitats; and (iii) DNA repair pathways (RADX proteins) supporting longevity and UV resistance. Tissue-specific expression profiling confirmed tentacle-exclusive localization of sensory receptors, directly linking genomic adaptations to foraging behavior. This study provides foundational insights into the evolution of a keystone marine predator, offering actionable genetic targets for conservation strategies and illuminating mechanisms that shape predator-prey coevolution in coral reefs.

Advances in mass spectrometry (MS)-based proteomics have enabled the large-scale characterization of posttranslational modifications (PTMs) through affinity-based enrichment. However, this technique introduces a bias towards selectively enrichable modifications, thus leaving oxidative modifications underexplored. Methionine oxidation (methionine sulfoxide) is an important indicator of cellular redox status, but its systematic analysis remains challenging because no enrichment method is available and artifactual oxidation can occur during sample preparation. Here, we developed an enrichment-free proteomic strategy for large-scale detection of methionine oxidation using a deep LC-MS platform. By optimizing acquisition conditions, we identified more than 260k precursors in a single-shot analysis. Under these conditions, methionine oxidation was efficiently detected, whereas many other PTMs remained poorly detected. To improve data reliability, we established a sample preparation workflow that minimized artifactual oxidation. Accordingly, we identified more than 3,500 methionine-oxidized proteins. Integration of methionine oxidation and expression proteomics across subcellular compartments revealed redox patterns under low-serum conditions, including increased mitochondrial oxidation and decreased endoplasmic reticulum oxidation. These changes are associated with metabolic reprogramming and altered antioxidant capacity. Overall, this study established an enrichment-free framework for the proteome-scale methionine oxidation analysis, and demonstrated that integrating oxidation and expression data enables the spatially resolved interpretation of cellular redox states.

Chromosome-scale genome assemblies in gymnosperms have lagged behind those of angiosperms, likely due to their large genomes. Coniferous tree species, which belong to the gymnosperms, are important resources for wood production in the forestry industry. To elucidate the evolution and speciation of these species and establish genome resources for breeding, we integrated draft assemblies with optical and genetic mapping to construct chromosome-scale genomes for Japanese cypress (Chamaecyparis obtusa, 8.7 Gb), Japanese cedar (Cryptomeria japonica, 9.6 Gb), and Chinese fir (Cunninghamia lanceolata, 13.4 Gb). Additionally, we assembled and annotated their chloroplast and mitochondrial genomes. Comparative analysis of the nuclear genomes revealed that while synteny is largely conserved, distinct translocations and inversions occurred in chromosomes 2, 6, and 9. Notably, the significantly larger genome of Cu. lanceolata was associated with frequent tandem gene duplications rather than transposon expansion. These findings suggest that chromosomal rearrangements and segmental duplications played key roles in the divergence of these species. The genomic resources presented here including chromosome-scale sequences, gene annotations, and genetic maps will facilitate advanced conifer genetics and accelerate forest tree breeding programmes.

Repetitive DNA sequences, as transposable elements (TEs) and satellite DNA (satDNA) spread and diversify within host genomes, impacting genome biology in numerous ways. In the first part of this review, we emphasize the evolutionary importance of satDNAs and TEs, providing a short summary of their roles and the mechanisms by which they influence the structure and function of genomes. We also discuss the broad, complex, and extensive relationships between TEs and satDNAs. Following that, we bring together different mechanisms on the generation of satDNA from TE, as it has been demonstrated that almost any part of any type of TE can undergo tandemization and produce novel satDNAs. Importantly, we here present a hypothesis that would explain the existence of particular types of monomers, namely composite satDNA monomers which display multiple subsequent stretches of similarity to various TEs, for which the explanation was lacking so far. We propose that even highly shuffled and degraded TE remnants residing in heterochromatin 'TE graveyards' can give rise to new satDNA sequence monomers, transforming these genomic loci into DNA 'recycling yards'. Furthermore, we emphasize important evolutionary questions regarding the causes, mechanisms, and frequency of these occurrences.

Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.

RNA-Seq data analysis is commonly biased towards detecting differentially expressed genes and insufficiently conveys the complexity of gene expression changes between biological conditions. This bias arises because discrete count models cannot fully and independently parameterize the mean, variance, and skewness of gene expression distributions. Therefore, a unified statistical framework that simultaneously tests differential expression, variability, and skewness is needed. We present SIEVEseq, a statistical methodology that provides such a framework. SIEVEseq embraces a compositional data analysis strategy to transform discrete RNA-Seq counts into continuous form with a distribution well-fitted by the skew-normal distribution. Both parametric and nonparametric simulations show that SIEVEseq better controls the false discovery rate and Type II error than existing differential expression methods. Analysis of the Mayo RNA-Seq dataset for Alzheimer's disease demonstrates that gene sets with significant differences in mean, variance, and skewness between control and disease groups strongly predict disease state. Furthermore, functional enrichment analysis indicates that relying solely on differentially expressed genes identifies only part of the biological spectrum, whereas incorporating genes with differential variability and skewness reveals additional disease-related aspects. Cross-data and cross-methodology validation suggest the detected biological signals are genuine. The SIEVEseq R package is available at https://cran.r-project.org/web/packages/SIEVEseq.

Sauvagesia rhodoleuca is an endangered species endemic to southern China. Due to human activities, only 6 fragmented populations remain in Guangdong and Guangxi. Despite considerable conservation efforts, its demographic history and evolution remain poorly understood, particularly from a genomic perspective. To address this, we assembled a chromosome-scale genome of S. rhodoleuca using Nanopore long-read sequencing, DNA short-read sequencing, RNA-seq, and Hi-C data. A total of 290.37 Mb of assembled sequences, accounting for 99.76% of the genome, were successfully anchored to 19 pseudo-chromosomes, achieving a BUSCO completeness of 98.40% and a long terminal repeat assembly index of 17.28. Genome annotation identified 26,758 protein-coding genes and 369 tRNA genes. Demographic analysis revealed a sharp decline in the effective population size of S. rhodoleuca beginning approximately 1 million years ago. Whole-genome duplication (WGD) analysis revealed that S. rhodoleuca experienced a whole-genome triplication (WGT) followed by a more recent WGD after diverging from the Rhizophoraceae. Genes retained from WGT and WGD events played key roles in the development and survival of S. rhodoleuca, as indicated by Gene Ontology analysis. The high-quality genome of S. rhodoleuca provides insights into its genomic characteristics and evolutionary history, offering a valuable resource for conservation and genetic management.

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and they offer valuable systems for analysing the genetic basis of adaptation to diverse habitats and the evolution of chromosomal organization. Genomic studies on cartilaginous fishes were initiated early with holocephalans because of their compact genomes, but have concentrated primarily on the family Callorhinchidae. Here, we focused on the most species-rich holocephalan family Chimaeridae and characterized the genome of its member, silver chimaera (Chimaera phantasma), in pursuit of genomic traces of adaptation to deep-sea vision. The resulting genome assembly exhibited high continuity and completeness, enabling the first chromosome-level comparison among holocephalans. They displayed substantial intragenomic variation in chromosome length, correlated with intron size, alongside a high degree of one-to-one chromosomal homology. Our search for silver chimaera photoreceptor genes revealed a shrunken set of opsin genes, including rhodopsin exhibiting a sequence signature typical of deep-sea adaptation. We also performed whole-genome resequencing of multiple silver chimaera individuals of both sexes, which identified a putative X-chromosome fragment. This is the first evidence of a holocephalan sex chromosome and suggests male heterogametic sex determination. Our findings contribute to a deeper understanding of vertebrate genome diversity and lay the groundwork for future genetic studies on this species.

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of 2 wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. A syntenic analysis of the G. hybrida genome and published Asterales genomes demonstrated that Gerbera has undergone a whole-genome triplication. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

Polyrhachis lamellidens is a temporary socially parasitic ant. The newly mated P. lamellidens queen takes over a colony of several Camponotus ant species and uses the labour of the host workers in the early stages of social parasitism. To facilitate genomic resources for these species, we assembled and annotated the chromosomal genome of P. lamellidens using the 10× Genomics linked-read and Hi-C sequencing, and the draft genome of its host, Camponotus japonicus, using long-read sequencing with the Revio system. The P. lamellidens chromosomal genome assembly is 214.1 Mb, 95.5% BUSCO completeness, and contains 13,703 protein-coding genes. The C. japonicus draft genome assembly is 314.2 Mb, 99.0% BUSCO completeness, and contains 11,207 protein-coding genes. Genome-wide phylogeny and synteny analysis confirmed the phylogenetic position of P. lamellidens and C. japonicus, and a high level of synteny with the genome of both ant species. In addition, P. lamellidens possesses nearly identical chemosensory proteins to its host, C. japonicus, and these genes tended to exhibit higher expression levels in the newly mated queen. The genome assemblies of P. lamellidens and its host C. japonicus provide a valuable resource for the molecular biological and bioinformatic basis for studying the strategy of social parasitism in ants.

Ascomycetes fungi produce carbohydrate-active enzymes that are prized in the biofuel industry. Comparative genome analysis of endophytic fungus Apiospora malaysiana with seven other closely related high quality genomes of endophytic and pathogenic organisms reveal that effectors and pathogenicity-related genes are predominantly localized within rapidly evolving gene-sparse regions rather than in the conserved region. This suggests bipartite genome architecture where the rapidly evolving region plays a role in host adaptation. Endophytic fungi adapt to plant invasion by enriching enzymes that degrade cellulose, hemicellulose, lignin, and pectin. In contrast, we observed that pathogenic fungi, especially N. oryzae, show a reduced number of secondary metabolites biosynthesis and catabolic genes, reflecting lifestyle adaptation. The presence of exclusive sporulating gene clusters in pathogen species could possibly indicate their pathogenic affiliation. Limited genome plasticity and low heterozygosity in A. malaysiana are in line with its predominant asexual life cycle choices in lab conditions. The secretome of A. malaysiana grown in cellulose-only media had more cellulase activities when compared to cultures grown in YPD media. Genes that were differentially up-regulated in cellulose-only media exhibited strong cellulose-degrading activity and genes involved in evading detection by the hosts surveillance system. Successful cloning and expression of selected CAZymes in bacterial expression systems with desirable physicochemical properties highlight the biotechnological potential of A. malaysiana for sustainable cellulolytic enzyme production. These findings position endophytes as valuable resources for cellulolytic enzyme research and broader bio-industrial applications.