Biology subjects

Hirakawa, H.

Publications and source records attributed to Hirakawa, H..

At least 19 recordsLinked to original sources

bioRxiv2026

A naturally occurring frameshift mutation in the UNUSUAL FLORAL ORGANS gene associated with the marimo floral phenotype in gerbera

BackgroundThe capitulum of Asteraceae is a highly specialized inflorescence whose formation requires the coordinated regulation of multiple developmental processes, including floral organ identity and floral meristem determinacy. The LEAFY (LFY)-UNUSUAL FLORAL ORGANS (UFO) regulatory module is known to play an important role in flower development; however, naturally occurring mutations affecting this pathway have not been genetically characterized in gerbera (Gerbera hybrida). ResultsIn this study, we characterized a novel gerbera mutant identified during a commercial crossing program and named it marimo based on its green, spherical capitulum. Morphological observations revealed the repeated formation of secondary and tertiary floret-like organs within primary floret-like organs. Scanning electron microscopy showed that the epidermal structure of the green organs in marimo was similar to that of wild-type involucral bracts. RNA sequencing identified numerous differentially expressed genes between marimo and the wild type, and network and Gene Ontology analyses highlighted gene groups associated with flower development, reproductive organ differentiation, and tissue structure formation. RNA-seq analysis showed increased expression of LFY and reduced expression of GGLO1, a PISTILLATA/GLOBOSA-like B-class MADS-box gene, in the marimo mutant. RT-qPCR analysis of a segregating population further confirmed reduced GGLO1 expression in marimo-type individuals. In addition, a single-nucleotide deletion was identified in the coding region of UFO. This deletion was predicted to cause a frameshift and a premature stop codon. In selfed progeny of No. 251, the UFO genotype was fully associated with capitulum phenotype, and only individuals homozygous for the mutant allele exhibited the marimo phenotype. ConclusionsThese results indicate that the naturally occurring frameshift mutation in UFO is the strongest candidate variant underlying the marimo phenotype. RNA-seq analysis showed increased LFY expression and markedly reduced GGLO1 expression in the marimo mutant. Reduced activity of the LFY-UFO regulatory module may therefore have altered the expression of GGLO1 and other floral organ development-related genes despite the continued expression of LFY. These changes may have affected both floral organ identity and floral meristem determinacy, resulting in the formation of green involucral bract-like organs and the repeated production of floret-like organs. The marimo mutant provides a useful genetic resource for investigating capitulum development in Asteraceae and may also serve as breeding material for introducing novel ornamental traits into gerbera.

genetics↗

bioRxiv2026

Hydration Energetics Shape Antibody Discrimination between Sulfotyrosine and Phosphotyrosine

Chemically similar post-translational modifications can mediate distinct biological functions, but how proteins distinguish between them remains unclear. Sulfotyrosine (sTyr) and phosphotyrosine (pTyr) exemplify this problem because they have similar sizes, local geometries, and electrostatic properties but function in different biological contexts. Here, we used the monoclonal antibody PSG2, which recognizes sTyr independently of the surrounding peptide sequence, to examine how a protein distinguishes these modifications. The crystal structure of PSG2 bound to an sTyr-containing peptide revealed a deep electropositive pocket with no modeled water molecules in direct contact with the sulfate group. Gas-phase density functional theory calculations favored pTyr over sTyr, showing that direct protein-ligand interactions alone are insufficient to explain PSG2 selectivity. Explicit first-shell hydration calculations showed that pTyr has a larger desolvation penalty than sTyr, and accounting for this difference reversed the calculated energetic order. Isothermal titration calorimetry showed favorable enthalpic and entropic contributions to sTyr binding, whereas no detectable heat signal was observed for pTyr. These results show that PSG2 distinguishes sTyr from pTyr through the balance between direct protein-ligand interactions and ligand desolvation.

biophysics↗

bioRxiv2026

Transposon insertion sequencing identifies genetic determinants of intrinsic rifamycin resistance in Mycobacterium abscessus

Mycobacterium abscessus exhibits intrinsic resistance to many antimicrobial agents, including rifampicin, a frontline anti-tuberculosis drug, severely limiting treatment options. Here, we used transposon insertion sequencing (Tn-Seq) to perform a genomewide screen to identify genes required for intrinsic rifampicin resistance in M. abscessus. We uncovered candidate genes that confer intrinsic resistance to the rifamycin-class antibiotics, rifampicin and rifabutin. The genes we identified included previously reported genes such as arr, helR, and MAB_2807. By comparing our results with the rifampicin intrinsic resistance gene in Mycobacterium tuberculosis, we found that the mechanisms underlying rifampicin intrinsic resistance were distinct between the two species. The contribution of seven representative candidate genes to rifampicin resistance was confirmed by characterizing targeted gene deletion or transposon insertion mutants. Among these determinants, MAB_2807 was identified as a major efflux-based contributor to rifamycin resistance, and its disruption increased intracellular rifampicin accumulation. In addition to known resistance determinants, Tn-Seq revealed contributions from many genes involved in cell envelope processes to rifamycin resistance. Guided by this genetic signature, we evaluated the combined effects of cell wall-targeting antimicrobial agents with rifamycins. We found that rifamycins displayed selective synergistic interactions with specific {beta}-lactam antibiotics. Interestingly, we found that rifamycin exposure altered cell envelope ultrastructure and increased the accumulation of the peptidoglycan precursor UDP-N-acetylglucosamine, suggesting that rifampicin perturbs envelope-associated metabolic homeostasis. These findings highlight rifamycin-induced vulnerable cellular processes that may inform rational combination strategies. ImportanceRifamycins are cornerstone antibiotics for the treatment of mycobacterial infections, yet they are ineffective against Mycobacterium abscessus. Although several key resistance mechanisms have been described, the full genetic basis of intrinsic rifamycin resistance remains to be elucidated. Here, we used transposon insertion sequencing to systematically identify genes that contribute to intrinsic rifamycin resistance in M. abscessus. Because recent studies have shown that chemical modification of rifamycins can overcome specific intrinsic resistance mechanisms, a comprehensive understanding of these determinants could facilitate the development of next-generation rifamycins with improved activity against M. abscessus. In addition, we unexpectedly found that rifamycin exposure alters cell envelope structure, the intracellular levels of a key metabolic intermediate in peptidoglycan biosynthesis, and susceptibility to certain {beta}-lactams in M. abscessus. These findings may help guide the rational development of combination therapeutic strategies with next-generation rifamycins.

microbiology↗

bioRxiv2026

Enabling Stable Cortical Reconstruction in the HCP Pipeline at Standard Resolution Using FastSurfer Integration with Hybrid T2w- and T1w-based Masking

This study aimed to enable stable cortical reconstruction within the Human Connectome Project (HCP) pipeline under standard-resolution (1 mm3) conditions by developing an integrated framework combining FastSurfer with a hybrid T2w- and T1w-based masking strategy. We implemented a FastSurfer-integrated HCP pipeline incorporating a hybrid masking approach (t2log-hybrid) to stabilize cortical reconstruction, where SynthStrip-derived masks were refined using log-transformed T2-weighted and squared T1-weighted images. An anterior commissure-anchored spatial switching mechanism selectively replaced artifact-prone T2w regions with T1w-derived information in orbitofrontal areas. Performance was evaluated against FreeSurfer v6 (FS6), v7 (FS7), and FastSurfer using geometric agreement, regional consistency, and vertex-wise thickness-myelin analyses. The proposed framework reduced total processing time by over 50% compared with FS6 and maintained high geometric agreement with modern pipelines (vertex-wise r = 0.970 vs FastSurfer; r = 0.929 vs FS7). Agreement with FS6 was lower (r = 0.842), reflecting systematic differences in boundary definition rather than random error. The hybrid masking approach showed higher regional consistency and lower variability in T1w/T2w-derived myelin estimates (CV = 16.50% vs 40.56% in FastSurfer), with more spatially consistent thickness-myelin interaction patterns in artifact-prone ventral regions. Integrating FastSurfer into the HCP pipeline with hybrid T2w- and T1w-based masking enables stable cortical reconstruction by constraining signal-driven instability while preserving algorithm-dependent spatial organization. These findings highlight the importance of masking as a constraint on instability in cortical reconstruction and support the applicability of HCP-style analysis to clinical and legacy MRI datasets.

neuroscience↗

bioRxiv2026

Tracing the emergence of the novel fluoroquinolone resistance gene qrtA in enterococci through environmental reservoirs and pELF-type linear plasmids

As animal hosts adapted to land, Enterococcus species diverged from a common ancestor shared with Vagococcus species by acquiring genes essential for survival and transmission in the exposed arid environment. In addition to their intrinsic ruggedness, human-associated enterococci now frequently exhibit multidrug resistance, largely driven by the accumulation of antimicrobial resistance genes (ARGs) on mobile genetic elements (MGEs). However, the source of these resistance elements, their diversity in natural reservoirs, and the risk that they pose remain unclear. To investigate the movement of novel ARGs from the environmental reservoir and the elements that convey them into clinically important enterococcal lineages, we examined environmental vancomycin-resistant enterococci (VRE) circulating in a polluted urban river in Hanoi, Vietnam. Whole-genome sequencing of VRE isolates revealed multidrug-resistance pELF-type linear plasmids harboring a novel fluoroquinolone resistance gene (qrtA) encoding a major facilitator superfamily transporter. The qrtA gene appears to have originated on Vagococcus chromosomes and to have been mobilized by IS1216E-associated MGEs. Vagococcus genomes show strong associations between ARGs, IS1216E, and plasmids related to those in enterococci, and conjugation experiments demonstrated that pELF-type linear plasmids can transfer between Enterococcus and Vagococcus without major fitness costs, positioning them as plausible vehicles for importing environmental ARGs into enterococci. Reconstruction of pELF-type linear plasmid evolution in the environment, together with database mining of rare qrtA-positive clinical isolates from Asia and Europe, suggests that qrtA-bearing pELF-type linear plasmids are in an early phase of global dissemination. These findings highlight the need for coordinated international One Health surveillance of ARG and MGE dynamics, including emerging determinants such as qrtA, together with proactive interventions to limit their spread.

microbiology↗

bioRxiv2026

Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species

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 C. 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 programs.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

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 two 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. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗

bioRxiv2025

Molecular evolution of terpene synthase underlying the diversification of isoprene emission in Fagaceae

Plants emit a wide range of volatile organic compounds, among which isoprene is the most abundant and atmospherically influential. Although oak species are major contributors to isoprene emission, there is considerable variation in isoprene emission capacity within the Fagaceae family. To unravel the evolutionary origins of isoprene emission, we investigated the molecular evolution of terpene synthase (TPS) genes across eight species within the Fagaceae. We identified a Fagaceae-specific TPS-b subclade in which potential isoprene synthase (IspS) activity evolved independently in two gene lineages within subgenus Quercus. Ancestral sequence reconstruction revealed that the acquisition of a diagnostic amino acid residue for IspS function arose convergently in these lineages and was subject to positive selection, suggesting adaptive evolution. Ancestral-enzyme assays targeting the gene lineage with high gene expression revealed that the early protein primarily produced monoterpenes from geranyl diphosphate (GPP), whereas their descendants shifted substrate preference to dimethylallyl diphosphate (DMAPP), evolving into dedicated isoprene synthases. Our results indicate that IspS activity was not ancestral in Fagaceae, but evolved approximately 56 million years ago within the subgenus Quercus, and has been retained ever since. These findings emphasize the roles of enzyme structural innovation and regulatory shifts in the diversification of volatile terpenoid biosynthesis.

evolutionary biology↗

bioRxiv2025

Transcriptome comparison between the cultured and in vivo Chick Primordial Germ Cells by SMART-seq-based single cell RNA sequencing

Primordial germ cells (PGC), the precursors of the germline, have unique cellular characteristics to undergo long-distance migration to the embryonic gonads and have the potential to differentiate into somatic cells. Among the animal models studying PGC development, the chicken PGCs are an ideal model, since it is a rare model in which long-term PGC cultivation is applicable. Although the cultural applicability of chicken PGC makes it attractive for revealing the PGC character and its developmental processes, some differences from endogenous PGCs are known, such as the remarkable up-regulation of cell proliferation and a lesser ability to reach the gonads. Understanding these differences at the molecular level is crucial. To this end, we first performed SMART-seq-based single-cell RNA sequencing to compare transcriptomes between endogenous PGCs and cultivated PGCs. Our results revealed that PGC cultivation causes a shift from a MYC-dependent to a MYCN-dependent gene regulatory network in PGCs, suggesting that this reprogramming contributes to the acquisition of proliferation ability and stem cell characteristics in cultivated PGCs. Additionally, our results suggest that the MYCN-dependent gene regulatory network increases the risk of somatic differentiation, particularly in neural fate, in cultivated PGCs. In addition, our transcriptome analysis identified new cell populations that show molecular character as intermediate cell states between germline and pluripotent cells from the early embryonic stage. Thus, our study provides fundamental molecular information to understand both the effects of PGC cultivation and the developmental process of chicken PGCs.

developmental biology↗

bioRxiv2025

The evolution of gene expression in seasonal environments

The biological activities of organisms are closely linked to seasonality. Phenology, the temporal orchestration of biological activities, is governed by gene expression, yet the evolutionary dynamics underlying seasonal gene expression remain unclear. To investigate these dynamics, we compared genome-wide expression dynamics (molecular phenology) in four dominant evergreen Fagaceae species in Asia (Quercus glauca, Q. acuta, Lithocarpus edulis, and L. glaber), using leaf and bud tissues over two seasonal cycles. We assembled high-quality reference genomes, identifying 11749 single-copy orthologous genes. Seasonal transcriptomic profiling of these orthologous genes revealed highly conserved gene expression across species in winter when temperatures fall below [~]10{degrees}C. Rhythmic gene expression with significant periodic oscillations was more prevalent in buds (51.9%) than in leaves (40.6%), with most rhythmic genes (78.4-92.0%) exhibiting annual periodicity, while a smaller fraction (1.2-11.9%) followed half-annual cycles. The seasonal peaks of rhythmic genes were highly synchronized across species in winter but diverged during the growing season, reflecting species-specific timing of leaf flushing and flowering. These findings suggest that the four species share a common molecular calendar in winter, which constrains the evolution of gene expression under seasonal environments. Impact StatementA comparative analysis of genome-wide seasonal gene expression dynamics across four forest tree species revealed that a shared "molecular calendar" emerges in winter, constraining gene expression evolution and potentially limiting temporal niche partitioning and species divergence in seasonal environments.

evolutionary biology↗

bioRxiv2025

Unstable anthocyanin pigmentation in Streptocarpus sect. Saintpaulia (African violet) is due to variant selectivity of a single MYB gene

O_LISaintpaulia (African violet) pigmentation is notoriously unstable, particularly following passage through tissue culture, but the instability mechanism is unknown. White-striped petals were thought to be due to epigenetics, but the genes involved are unknown. We confirmed that white stripes result from epigenetic regulation based on the flower color traits of plants obtained from tissue culture. C_LIO_LIGene expression in several plant lines, anthocyanin quantification, bisulfite sequencing, and methylation analyses were used to demonstrate the presence of a single MYB gene responsible for pigment variation. We identified SiMYB2 as the cause of variations in tissue color patterning, and that two RNAs were generated from SiMYB2. SiMYB2-Long was expressed in colored tissues, while SiMYB2-Short was expressed only in non-colored tissues. Functional analyses revealed that SiMYB2-Long is an anthocyanin biosynthesis activator and SiMYB2-Short is non-functional. Exon 3 of SiMYB2 was generated by the insertion of a transposon-like sequence. A mutant lacking the element was obtained from cultivars with non-colored tissues. Anthocyanin content and SiMYB2-Long expression in the mutant were greatly increased compared to wild type. C_LIO_LIOur results suggest that the white-striped petals of Saintpaulia are not formed by periclinal chimeras but thorough the transcriptional selectivity of epigenetically regulated SiMYB2. C_LI

plant biology↗

bioRxiv2024

Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated

Quinoa, an annual allotetraploid plant native to the Andean highlands of South America, is emerging as an important seed crop for global food and nutrition security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats (Gypsy and Copia), representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 64,945 and 65,303 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.

plant biology↗

bioRxiv2023

Establishing a comprehensive web-based analysis platform for Nicotiana benthamiana genome and transcriptome

Nicotiana benthamiana has long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.1 Gb genome, 57,583 genes have been annotated within a 61 Mb region. We created a comprehensive and easy-to-use platform to use transcriptomes for modern annotation. These tools allow to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads. To demonstrate their utility, we analyzed the gene expression profiles of enzymes within the nicotine biosynthesis pathway, a secondary metabolic pathway characteristic of the Nicotiana genus. Using the developed tool, expression profiles of the nicotine biosynthesis pathway genes were generated. The expression patterns of eight gene groups in the pathway were strongly expressed in the roots and weakly expressed in leaves and flowers of N. benthamiana. The results were consistent with the established gene expression profiles in Nicotiana tabacum and provided insights into gene family composition and expression trends. The compilation of this database tool can facilitate genetic analysis of N. benthamiana in the future. Significance statementA tool was developed to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads of Nicotiana benthamiana. The database developed using the tool can evolve into a comprehensive all-in-one analysis platform by continuously incorporating transcriptome data released to date, newly released RNA-seq data, and annotations in the future.

plant biology↗

bioRxiv2022

Haploid-resolved and chromosome-scale genome assembly in hexa-autoploid sweetpotato (Ipomoea batatas (L.) Lam)

Sweetpotato (Ipomoea batatas (L.) Lam) is the worlds seventh most important food crop by production quantity. Cultivated sweetpotato is a hexaploid (2n = 6x = 90), and its genome (B1B1B2B2B2B2) is quite complex due to polyploidy, self-incompatibility, and high heterozygosity. Here we established a haploid-resolved and chromosome-scale de novo assembly of autohexaploid sweetpotato genome sequences. Before constructing the genome, we created chromosome-scale genome sequences in I. trifida using a highly homozygous accession, Mx23Hm, with PacBio RSII and Hi-C reads. Haploid-resolved genome assembly was performed for a sweetpotato cultivar, Xushu18 by hybrid assembly with Illumina paired-end (PE) and mate-pair (MP) reads, 10X genomics reads, and PacBio RSII reads. Then, 90 chromosome-scale pseudomolecules were generated by aligning the scaffolds onto a sweetpotato linkage map. De novo assemblies were also performed for chloroplast and mitochondrial genomes in I. trifida and sweetpotato. In total, 34,386 and 175,633 genes were identified on the assembled nucleic genomes of I. trifida and sweetpotato, respectively. Functional gene annotation and RNA-Seq analysis revealed locations of starch, anthocyanin, and carotenoid pathway genes on the sweetpotato genome. This is the first report of chromosome-scale de novo assembly of the sweetpotato genome. The results are expected to contribute to genomic and genetic analyses of sweetpotato.

genomics↗

bioRxiv2022

Haplotype-resolved de novo genome assemblies of four coniferous tree species

Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we optimized the DNA library preparation protocols and employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, and Cunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in C. obtusa to 16.0 Mb in L. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3-95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

genomics↗

bioRxiv2022

Enterococcal linear plasmids adapt to Enterococcus faecium and spread within multidrug-resistant clades.

Antimicrobial resistance (AMR) of bacterial pathogens, including enterococci, is a global concern, and plasmids are crucial for spreading and maintaining AMR genes. Plasmids with linear topology were recently identified in clinical multidrug-resistant enterococci. The enterococcal linear-form plasmids, such as pELF1, confer resistance to clinically important antimicrobials, including vancomycin; however, little information exists about their epidemiological and physiological effects. In this study, we identified several lineages of enterococcal linear plasmids that are structurally conserved and occur globally. pELF1-like linear plasmids show plasticity in acquiring and maintaining AMR genes, often via transposition with the mobile genetic element IS1216E. This linear plasmid family has several characteristics enabling long-term persistence in the bacterial population, including high horizontal self-transmissibility, low-level transcription of plasmid-encoded genes, and a moderate effect on the Enterococcus faecium genome alleviating fitness cost and promoting vertical inheritance. Combined with its broad host range, the linear plasmid is an important factor in the spread and maintenance of AMR genes among enterococci.

microbiology↗

bioRxiv2021

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in family Gentianaceae

Eustoma grandiflorum (Raf.) Shinn., is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. The 36 pseudomolecules and unplaced 64 scaffolds were created with total length of 1,324.8 Mb. Full-length transcript sequencing was obtained by PacBio Iso-Seq sequencing for gene prediction on the assembled genome, Egra_v1. A total of 36,619 genes were predicted on the genome as high confidence HC) genes. Of the 36,619, 25,936 were annotated functions by ZenAnnotation. Genetic diversity analysis was also performed for nine commercial E. grandiflorum varieties bred in Japan, and 254,205 variants were identified. This is the first report of the construction of reference genome sequences in E. grandiflorum as well as in the family Gentianaceae.

genomics↗

bioRxiv2021

A chromosome-level genome sequence of a model chrysanthemum: evolution and 1 reference for hexaploid cultivated chrysanthemum

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspread repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to a relatively large genome size. Furthermore, we identified aretrotransposon, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

plant biology↗