DNA Research

As an important cultivated red alga, Gracilariopsis lemaneiformis has great economic and ecological value. However, its existing genome assembly is highly fragmented and inadequately annotated. In this study, we constructed the first high-quality chromosome-level genome of Gp. lemaneiformis using PacBio long reads, Illumina short reads and Hi-C sequencing data. The assembled genome was approximately 86.66 Mb and the assembled sequences were anchored to 28 pseudo-chromosomes with lengths ranging from 1.70 to 7.81 Mb. 99.91% of the PacBio reads could be mapped to our assembly. In total, 8,664 genes were annotated, and the repeat elements identified in Gp. lemaneiformis constituted 65.04% of the whole genome, including 2.24% tandem repeat sequences and 62.81% interspersed repeats. We also established a high-evidence phylogenetic tree from 19 representative algae species, with the main aim to calculate their divergence times. This high-quality genome of Gp. lemaneiformis provides a crucial foundation for understanding genetic characteristics, investigating the genomic evolution, and facilitating molecular breeding.

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

As one of the earliest-diverging multicellular eukaryotic lineages, the bladed Bangiales (Rhodophyta) possess a deep evolutionary history with a central role in the multi-billion-dollar global seaweed aquaculture industry. Although North Atlantic representatives are emerging candidates for regional mariculture, the scarcity of high-quality genomic resources for these taxa hinders both fundamental research and commercial optimization. To address this, we present the first chromosome-level genome assemblies for two native European species: Porphyra dioica (150.44 Mbp) and Porphyra linearis (95.22 Mbp). By integrating Oxford Nanopore Technologies (ONT) long-read sequencing with Hi-C proximity ligation, we generated highly contiguous nuclear genomes resolved into five chromosomes. Structural gene models were predicted through the BRAKER3 pipeline, identifying 12,548 and 10,382 protein-coding genes for P. dioica and P. linearis, respectively. Subsequent homology-based functional annotation characterized 57.4% and 59.8% of these predicted proteins. Supplemented by circularized organellar genomes, these reference genomes provide a critical framework for future research, enabling comparative studies of Atlantic-Pacific divergence and facilitating the development of selective breeding programs for sustainable European aquaculture.

Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.

Gene model for the ortholog of Lst8 (Lst8) in the May 2011 (WUGSC dyak_caf1/DyakCAF1) Genome Assembly (GenBank Accession: GCA_000005975.1) of Drosophila yakuba. This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

The nematode Caenorhabditis elegans was the first metazoan to have its genome completely sequenced and assembled. Since that time, researchers have continuously updated the reference genome and manually curated its approximately 20,000 genes. The closely related species, Caenorhabditis briggsae, has served as a comparative model because of its similar morphology, mode of reproduction, and patterns of intra-species genetic variation. However, the genomic resources for C. briggsae lag behind C. elegans, hindering comparative genomics studies between the species. Decades of experimentation have been performed in the AF16 reference strain genetic background, so we obtained high-coverage long-read sequencing and high-throughput chromosome conformation capture data to create an updated reference genome for an isogenic derivative of AF16, named CGC2. The CGC2 genome is vastly improved relative to the existing AF16 assemblies, with no unplaced sequence, no gaps, and telomere-to-telomere contiguity. To provide genomic resources for CGC2, we exploited deep RNA-seq libraries from all developmental stages to predict protein-coding gene annotations comparable in accuracy and completeness to the existing AF16 gene models. We also performed lift-over of 108 validated insertion-deletion variants to the updated coordinate system of the CGC2 genome to facilitate future mappings of mutations. In summary, we present an updated reference genome for the canonical AF16 reference strain with improved genomic resources to enable high-quality intra- and inter-species comparative studies.

Nanopore sequencers have the potential to liberate DNA sequencing from centralized core facilities to distributed analytical nodes. Until now, Oxford Nanopore Technologies (ONT) has been the sole manufacturer of a portable nanopore sequencer, but analogous platforms are in production. Nanopore sequencers from Qitan Technology (QT) are widely used in China but have been unavailable outside that nation and lack independent performance testing. Enabled by early access to QTs least expensive sequencer and flow cell, the QNome-3841 and QCell-384, we tested whether they could generate accurate DNA barcodes cost-effectively. In several tests involving amplicon pools from 95 to 9,120 specimens, QT recovered valid DNA barcodes from nearly as many specimens (98%) as ONT. QT sequences had slightly lower fidelity than their ONT counterparts and QT frequently failed to resolve the correct length of G/C homopolymers. However, barcode sequences from the two platforms were nearly indistinguishable after bioinformatic treatment. QTs wash kit performed well, enabling a QCell to sequence eight amplicon pools with zero carryover between runs and minimal degradation of the flow cell. Its ultra-fast protocol allowed library preparation in a single step that could be completed in 15 minutes, but this came at the cost of lower quality data. Once widely available, QT devices will be well-suited for supporting DNA barcode analysis.

Oryza granulata Nees et Arn. ex Watt, a diploid wild rice (GG genome), possesses exceptional shade tolerance and is a key genetic resource for rice improvement. However, previous genome assemblies lacked continuity and completeness. Here we present a chromosome-scale reference genome of O. granulata using PacBio SMRT (113x), Hi-C (95x), and Illumina sequencing. The final assembly is ~764.24 Mb, with a scaffold N50 of ~59.32 Mb, and ~96.47% of the sequence anchored to 12 chromosomes. BUSCO completeness is ~98.6%. We annotated ~42,064 protein-coding genes, of which ~95.39% were functionally annotated, along with ~73.46% repetitive elements. The genome assembly and raw sequencing data are available at NGDC (PRJCA061980), NGDC GSA (CRA068332), and NGDC GWH (GWHISVE00000000.1). This high-quality genome will serve as a fundamental resource for evolutionary genomics, conservation biology, and breeding of shade-tolerant rice cultivars.

The marbled teal (Marmaronetta angustirostris) is a widely distributed but declining waterfowl species, classified as Near Threatened globally and Critically Endangered in Spain. Despite ongoing conservation actions, including ex situ management and population reinforcement programmes, the genomic consequences of long-term captivity, inbreeding, and patterns of functional genetic variation remain unknown due to the absence of a species-specific reference genome. Here, we present the first chromosome-level genome assembly for this species. The genome was generated using PacBio HiFi long reads and Omni-C data, yielding a 1.15Gb assembly with a scaffold N50 of 76.95Mb. A total of 97.16% of the assembly was anchored into 36 chromosome-scale scaffolds, including the Z and W sex chromosomes. BUSCO analysis recovered 99.2% of conserved avian genes. Gene prediction was performed using both ab initio and homology-based strategies, resulting in 16,048 protein-coding genes. This resource provides a foundation for genomewide analyses of inbreeding, demographic history, and adaptive variation, and will support evidencebased in situ and ex situ conservation strategies for this threatened species.

Polyploid genome assembly presents unique challenges due to extensive heterozygosity and complex haplotype structure. We report a haplotype-resolved, chromosome-scale assembly of Regen-SY27x, a genotype of autotetraploid alfalfa (Medicago sativa), which is widely used for genetic modification because of its excellent regenerative capacity in tissue culture. Using PacBio HiFi long reads, Omni-C scaffolding, and linkage map guided phasing, we generated a 3.2 GB assembly comprising four haplotypes with high contiguity and completeness. Kmer-based validation confirmed accurate haplotype separation, while linkage map integration and dotplot analysis identified and corrected chimeric scaffolds. Gene annotation yielded 221,688 protein-coding genes, with more than 99% assigned to pseudochromosomes. Repetitive elements accounted for 62.7% of the genome, dominated by long terminal repeat retrotransposons and a high fraction of Helitrons. The spatial enrichment of Helitrons within gene-dense distal chromosome arms underscores their pivotal role as key drivers of genomic innovation and gene family expansion. We identified 3,696 nucleotide-binding leucine-rich repeat R genes, with Toll/interleukin-1 receptor-like and Rx-type subclasses forming large tandem clusters across haplotypes. Comparative analyses revealed strong macrosyntenic conservation among Regen-SY27x and the publicly available Chinese alfalfa genomes but extensive structural variation both within Regen-SY27x haplotypes and between Regen-SY27x and the Chinese genotypes with tens of thousands of duplications, inversions, and translocations detected. These results demonstrate that a single autotetraploid individual captures extensive structural diversity, but individuals from different populations vary greatly. The Regen-SY27x assembly provides a foundational genomic resource for investigating polyploid genome evolution and identifying genetic variation relevant to biological and agronomic improvement in alfalfa. Article SummaryThis study presents the first chromosome-scale, haplotype-resolved genome assembly of the US alfalfa germplasm, Regen-SY27x, a key alfalfa genotype used widely for genetic engineering. We integrated HiFi long reads, Omni-CTM scaffolding, and linkage map-guided phasing to reconstruct all four haplotypes of this complex autotetraploid. Our results identified 221,688 protein-coding genes and reveal immense intra-individual structural variations dominated by small duplications. This high-quality reference serves as a foundational tool for the alfalfa community, enabling researchers to link complex structural diversity with agronomic traits and further enhance the biotechnological potential of this essential forage crop.

Cytochrome P450 monooxygenases (CYP450s) are key oxidative enzymes that diversify plant specialized metabolites and play a central role in the biosynthesis of bioactive withanolides in Withania somnifera (L.) Dunal. Despite their importance, genome-wide information on CYP450s in W. somnifera has remained elusive. Herein, the first high-quality genome assembly (2.2 Gb, scaffold N50: 47.4 kb) of an Indian W. somnifera cultivar was generated using a hybrid Oxford Nanopore-Illumina sequencing strategy. Comparative analysis with the NCBI reference genome revealed moderate SNP and indel variations, reflecting intraspecific genetic diversity. A comprehensive CYP450 catalog was established and analyzed phylogenomically across nine plant genomes, encompassing both withanolide-producing and non-producing Solanaceae and non-Solanaceae species. Unique CYP families (CYP450A, CYP1194, and CYP705A) were detected exclusively in W. somnifera, suggesting lineage-specific metabolic innovations, while Solanaceae-restricted (CYP82E/M) and absent (CYP81B, CYP6) lineages highlight taxonomic divergence. Across all analyzed genomes, 36 conserved CYP450 subfamilies, including triterpenoid-associated members, were identified, suggesting a shared oxidative framework adaptable to specialized metabolism. Moreover, potential candidate genes in the triterpenoid pathway, including CYP72A692_1, CYP72A560_4, CYP716A48, CYP724B2, and CYP51G1, were identified through phylogenetic integration with functionally validated triterpenoid-modifying enzymes from other plant species. Gene family evolution analysis further revealed contraction of monoterpenoid-related subfamilies (CYP76A), implying a metabolic shift toward triterpenoid specialization. The comprehensive genome assembly and CYPome of W. somnifera offer a valuable resource for functional characterization, evolutionary analysis, and the identification of genes underlying its specialized metabolism. Furthermore, the study advances our understanding of CYP450 diversity and evolution, revealing lineage-specific innovations, conserved subfamilies, and key candidate genes involved in triterpenoid biosynthesis. Together, these findings lay a foundation for future functional studies and pathway engineering aimed at optimizing the metabolic potential of this important medicinal plant.

Measles virus remains a significant global health threat, and despite the availability of an effective vaccine, measles cases continue to increase worldwide in recent years. Genomic surveillance has become an essential tool for monitoring virus circulation and investigating outbreaks. Here, we describe a wet-laboratory method for whole-genome sequencing of measles virus using a tiled amplicon approach and Illumina sequencing technology. A previously published Oxford Nanopore-based tiled primer scheme was adapted to include both circulating measles genotypes and for use on the Illumina platform. Two Illumina library preparation kits, Illumina DNA Prep (IDP) and Nextera XT (XT), were evaluated for performance. The IDP kit demonstrated more complete genomes and consistent genome coverage compared with XT. Using quantified reference genomes, the limit of detection was determined to be 10,000 genome copies for genotype B3 and D8. Sequence accuracy was evaluated using previously characterized clinical samples and showed high concordance. This method provides a reliable and sensitive approach for measles virus whole-genome sequencing using Illumina platforms and is suitable for genomic surveillance applications.

Obtaining tomato plants with firm and intact fruit is one of the main goals in tomato breeding programs. Achieving these goals through conventional breeding is time-consuming and can lead to the loss of unwanted traits. In other hand, consumers are concerned about the presence of transgenic elements in plants acquired through RNA interference. The use of CRISPR/Cas9 technology has made it possible to overcome the above-mentioned shortcomings. In this study, the {beta}-D-N-acetylhexosaminidase ({beta}-hex) gene, which is involved in tomato fruit ripening, was knocked out using CRISPR/Cas9. In the resulting mutant plant genome, an indel mutation was found in exons 1 and 2 of the {beta}-hex gene. Plants with a mutation in their genome were observed to have increased fruit firmness and shelf life compared to control plants without affecting fruit quality.

BackgroundUrtica dioica, also known as stinging nettle, is a widespread plant that can indicate high nitrogen availability in the soil. It is probably best known for the pain caused by touching it. U. dioica is also recognized as a medicinal plant with reports claiming applicability against numerous diseases. ResultsA highly continuous genome sequence was constructed based on nanopore long read sequencing data. The total assembly size is 1.1 Gbp with an N50 of 40.7 Mbp. RNA-seq data and hints from other species were integrated to produce a high quality annotation of the protein encoding genes. This genomic resource enabled the identification of genes involved in the flavonoid biosynthesis. A particular focus was on anthocyanin biosynthesis genes as these are crucial for high light and nitrogen deprivation stress response, which is revealed by redding of the leaves. ConclusionThis genomic resource provides the basis for future studies unraveling the biosynthesis pathways underlying various medically important compounds produced by stinging nettles.

Here, we present a comprehensive multiomics analysis of anthocyanin biosynthesis in Rubus armeniacus, known for its dark fruits. A phased genome sequence of the tetraploid blackberry was generated, achieving an N50 of 34 Mb with an assembly size of 1.2 Gbp based on Oxford Nanopore Technology sequencing (ONT). The BUSCO score for the total assembly shows a high completeness of 99.1%. The assembly was separated into 4 pseudohaplophases, with the pseudohaplophase A representing the R. armeniacus genome in 7 chromosome scale contigs, with an N50 of 46 Mbp and 98.8% conserved BUSCO genes. A total of 118,183 protein coding genes were annotated within the genome assembly and all relevant genes encoding enzymes and transcriptional regulators of the anthocyanin biosynthesis pathway were identified within each pseudohaplophase. To further understand the underlying cause of dark pigmentation, the gene expression was analysed during different stages of berry development revealing a strong induction of anthocyanin biosynthesis genes including the anthocyanin activating subgroup 6 MYB transcriptions during the berry ripening process. Further, a quantification of cyanidin-3-O-glucoside in methanolic berry extract, utilizing a UHPLC-HRAM-MS analysis, revealed an approximately 500-fold increase of cyanidin-3-O-glucoside from green to black fruit, indicating that dark pigmentation in R. armeniacus results from high anthocyanin accumulation. Significance statementThis study provides a multiomics analysis of the dark pigmentation of Rubus armeniacus, including a high quality phased assembly and an in-depth analysis of the anthocyanin biosynthesis pathway. A transcriptional and metabolomic analysis revealed that dark berry pigmentation is caused by a high accumulation of cyanidin-3-O-glucoside during fruit ripening.

Biolistic transformation is a versatile tool in plant science, yet high equipment costs and tissue damage from high-pressure gas remain significant barriers. Building on our previously developed "TSGMAC", a low-cost, helium-free biolistic system, we report three major advancements to enhance its throughput, delivery quality, and quantitative capability. First, a "guide barrel" assembled from commercial DIY fittings was developed; it effectively eliminates physical tissue damage and ensures uniform particle distribution, even in soft tissues like bok choy (Brassica rapa subsp. chinensis). Second, a rapid gene expression platform using PCR products was characterized. Results demonstrate that linear DNA constructs are efficiently circularized via non-homologous end joining (NHEJ) in plant cells, and protein expression is robust regardless of the relative positions of the promoter, coding sequence, and terminator. This system bypasses time-consuming cloning. Third, a cost-effective, highly sensitive dual-luciferase assay system utilizing teal Luc (teLuc) and inexpensive firefly luciferase (FLuc) inhibitors was established. This integrated workflow enables rapid, quantitative molecular biology using supermarket-obtained materials and standard PCR reagents. Our findings provide a practical foundation for plant scientists, synergistically accelerating gene functional analysis and genetic tool development.

O_LIPlants and fungi are major sources of natural products beneficial to society, making the study of distinct species essential for discovering new drugs and bioactive compounds. The medicinal mushroom "Lingzhi" or "Reishi" (Ganoderma lingzhi) is widely used in traditional medicine and extensively studied for its bioactive triterpenoids, yet it is commonly identified as Ganoderma lucidum, the type species of the genus, which lacks a type specimen. C_LIO_LIWe sequenced a G. lucidum specimen preserved in the Kew fungarium, which agreed with the original description and was collected from wood of Corylus avellana in southern England. Using this reference specimen, we compiled genomic and ITS barcoding datasets to explore the genetic and geographic variation within this species. C_LIO_LIWe showed that G. lingzhi and G. lucidum diverged more than 12 million years ago and that all seven "G. lucidum" genomes deposited in public databases belong to other species. More than 1000 barcoding sequences showed that the widely used homology-based ITS barcoding is not working in this group, which can be mitigated by a phylogenetic placement approach. The 149 sequences assigned to G. lucidum with high confidence showed a Eurasian distribution and introductions to North and South America and Africa. C_LIO_LIOur study underscores the importance of accurate species identification and provides guidance for a group of pharmaceutical and socially significant species. To further support future studies and the wider public in differentiating between G. lingzhi and G. lucidum, we propose using "False Lingzhi" as the English name for G. lucidum. C_LI Societal Impact StatementTraditional Chinese Medicine has expanded far beyond Asia, with growing markets in North America and Europe for supplements and functional foods. Lingzhi or Reishi (Ganoderma lingzhi), a well-known medicinal mushroom, is valued for its anti-inflammatory and anticancer properties. However, it is often misidentified with species that may not provide the same health benefits. This confusion poses risks to consumer safety, product regulation, and research. Here, we establish a reference using morphological and molecular tools for the most commonly misidentified species (Ganoderma lucidum) and propose the name "False Lingzhi" to distinguish it, supporting accurate identification, safer product development, and reliable research.

CRISPR-Cas genome editing toolkits have expanded the scope of genetic studies in various emerging model organisms. However, their applications are limited mainly to knockout experiments due to technical difficulties in establishing knock-in strains, which enable in vivo molecular tagging-based experiments. Here, we investigated knock-in strategies in the harlequin ladybug Harmonia axyridis, a model insect for evolutionary developmental biology, which shows more than 200 color pattern variations within a species. We tested several knock-in strategies using synthetic DNA templates. We found that ssDNA templates generated founder knock-in strains efficiently (2.5-11%), whereas the 5 regions of ssDNA templates were frequently deleted when the insert length exceeded [~]40 bases. To overcome this limitation, we designed several 3 extended DNA templates. Fast-annealed 3-extended double-stranded DNA templates, which were designed for tagging endogenous proteins with epitope tags, showed high founder generation efficiency (9.9-20.9%) and accuracy (30.8-85.7%). This strategy is also applicable to the two-spotted cricket Gryllus bimaculatus, suggesting that the fast-annealed 3-extended dsDNA template is a versatile DNA template for generating knock-in strains in emerging model insects for developmental genetic studies. Summary statementFast-annealed 3-extended dsDNA templates facilitate efficient CRISPR-Cas9-mediated knock-in in emerging model insects.

Taro (Colocasia esculenta (L.) Schott) is an important vegetable and food crop in China, but in recent years, soft rot disease has frequently occurred during its cultivation and production. This disease damages the underground corms and petiole bases of taro, causing decay in the affected parts and emitting a foul odor, leading to wilting and lodging of the entire plant. This has resulted in significant economic losses to taro production in China, along with food safety issues and ecological problems caused by excessive pesticide use, making it urgent to find a green and efficient control method. Due to its specificity and environmental safety, phage therapy exhibits advantages that chemical pesticides cannot match, representing a promising alternative to chemical pesticides for controlling pathogenic bacteria. In the preliminary work of this study, a bacterial strain was isolated from taro soft rot in Shaoguan, Guangdong, and initially identified as Pectobacterium colocasium ZXC0623. Using this strain as the host bacterium, a Pectobacterium phage was screened and named QJphage. We analyzed its physicochemical properties and obtained its biological characteristics, including optimal titer, optimal infection latency period, optimal infection multiplicity, optimal storage solvent, and resistance to ultraviolet light, pH, and chloroform. Through homologous alignment analysis, eight tail fiber proteins encoded in the QJphage genome were predicted as putative receptor-binding proteins (RBPs). To validate this prediction, the corresponding genes were cloned downstream of the egfp gene via homologous recombination, and the resulting recombinant plasmids were transformed into a prokaryotic host to express EGFP-tagged tail fiber fusion proteins. Fluorescence detection and confocal laser scanning microscopy confirmed that the protein encoded by ORF04 functions as the RBP. Furthermore, lipopolysaccharide (LPS) was knocked out in the host strain P. colocasium ZXC0623. Both{Delta} LPS1 and{Delta} LPS2 mutants formed smaller plaques compared to the wild-type strain, and the{Delta} LPS1 mutant additionally exhibited a significant reduction in plaque number, indicating that LPS serves as a receptor involved in QJphage adsorption. Finally, transcriptomic analysis during the latent period of infection focused on 20 genes predicted to be associated with phage-host receptor binding and anti-phage immune systems. The results revealed that pilin proteins act as potential reversible adsorption receptors for QJphage, while the host strain ZXC0623 also possesses a diverse repertoire of anti-phage defense systems. Collectively, QJphage exhibits stable physicochemical properties, a well-defined LPS-dependent infection mechanism, and a host with diverse defense systems, providing a foundation for the control of taro soft rot and future phage-related research. ImportancePhage therapy has emerged as a highly effective biocontrol strategy against Pectobacterium, with its specificity making it particularly valuable. A critical aspect of this approach is the identification of phage receptors. The initial step in the phage life cycle involves adsorption to the bacterial host, beginning with reversible contact followed by irreversible binding between phage receptor-binding proteins and specific bacterial surface receptors. Potential receptors include glycolipids in the Gram-negative outer membrane, capsular polysaccharides, and various membrane proteins or appendages. In this study, we first characterized the physicochemical properties of the isolated QJphage. Through integrated transcriptomic and whole-genome analyses, we demonstrated that the LPS of Pectobacterium specifically interact with the tail fiber proteins of QJphage. This research provides the first evidence revealing the molecular mechanism of interaction between Pectobacterium and its phage, establishing a foundation for developing phage-based control strategies against soft rot diseases.

The Leray-XT primer pair has been widely used to amplify the mitochondrial cytochrome c oxidase subunit I (COI) gene from animals. In some marine metabarcoding studies, protists have also been amplified and sequenced using these primers. Here, we ask if the Leray-XT COI primer pair is suitable for observing ciliates and radiolarians, which are numerically and ecologically important components of marine protistan communities. We show that while there are sufficient COI reference sequences for ciliates in NCBI for taxonomic assignments, there are currently only two COI reference sequences for radiolarians. Using in-silico analyses, we additionally show that while the reverse primer Leray-XT primer can bind and potentially amplify both ciliates and radiolarians, the forward primer cannot bind to either taxon. These results show that the Leray-XT primer pair is not suitable for observing ciliates and radiolarians, although it may be useful for observing other marine protistan taxa.