Biology subjects

Shimizu, K.

Publications and source records attributed to Shimizu, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Engineering robust cardiomyocyte differentiation from iPSCs through WNT-mediated process window expansion

Lack of robustness and high variability in cardiomyocyte (CM) differentiation from human induced pluripotent stem cells (hiPSCs) remain critical challenges for cardiac regenerative medicine and biological research. Guided by developmental principles of lineage specification, we investigated whether early WNT inhibition could expand the process window of CM differentiation and thereby improve robustness. To test this, we compared early WNT inhibition from days 1--5 with standard inhibition from days 3--5 following a 1-day CHIR99021 (CHIR) treatment for WNT activation. Focusing on CHIR concentration as a critical parameter, we found that early WNT inhibition substantially broadened the concentration window yielding [≥]80% differentiation efficiency across distinct hiPSC lines. Extending the analysis to a two-dimensional parameter space incorporating cell density revealed a markedly expanded [≥]80% process window. Temporal analysis of lineage-specific transcription factor expression showed that early WNT inhibition suppressed paraxial mesoderm (PM) specification, likely through MSGN1 suppression, in the range of high initial WNT activation that otherwise favored PM fate, thereby extending the process window. It also suppressed definitive endoderm (DE) specification within the expanded window, promoting a more favorable lateral plate mesoderm/cardiac fate. We further demonstrated substantially reduced variability under parameter perturbations and across wells and batches, accompanied by higher differentiation efficiency, without compromising CM phenotypes. These findings demonstrate early WNT inhibition as an effective strategy for expanding the process window of CM differentiation and improving robustness, while exemplifying the process engineering principle that a broader window can support more robust differentiation, with potential relevance to stem cell--based bioprocesses.

bioengineering↗

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

Active Nuclear Shuttling Enables Efficient Virus-Free CAR Gene Integration Using Ready-to-Use Lipid Nanoparticles

Non-viral engineering of chimeric antigen receptor T (CAR-T) cells is highly desirable to overcome the cost, safety, and scalability limitations associated with viral vectors and electroporation. However, efficient nuclear delivery and stable genomic integration of DNA in primary human T cells remain major challenges. Here, we established a virus-free CAR-T manufacturing platform using lipid nanoparticles (LNPs) combined with a nuclear localization signal (NLS) shuttle strategy. We developed proprietary ready-to-use LNPs that enable on-demand encapsulation of nucleic acids. To overcome nuclear transport barriers, NLS-fused transposase or genome-editing nuclease was used to bind donor DNA in the cytoplasm and promote active nuclear import. This approach enabled highly efficient and low-toxicity delivery of mRNA and plasmid DNA into primary human T cells. NLS-assisted transposase delivery markedly enhanced genomic integration of the CAR gene, resulting in high expression levels and improved cell viability compared with electroporation-based methods. In addition, TRAC locus-specific targeted integration was achieved more efficiently through end-joining-based repair pathways than through homology-directed repair following LNP delivery. The resulting engineered CAR-T cells exhibited potent and antigen-specific cytotoxic activity. Together, these results demonstrate that NLS-assisted LNP delivery overcomes a key bottleneck in non-viral gene integration and provides a robust strategy for the generation of functional CAR-T cells.

bioengineering↗

bioRxiv2026

Average local nucleosome motion remains constant during interphase in living human cells

BackgroundDynamic chromatin behavior, which is related to chromatin accessibility, plays a critical role in various genome DNA functions such as RNA transcription and DNA replication/repair. Previous studies using highly synchronized cells showed that average local chromatin motion, captured by single-nucleosome imaging and tracking on a second time scale, remained almost constant throughout G1, S, and G2 phases in living human cells, although possible effects of prolonged drug treatments for cell-cycle synchronization could not be excluded. ResultsTo avoid possible effects of prolonged drug treatment, we combined single-nucleosome imaging with Fucci probes to visualize cell-cycle progression through G1, S, and G2. Using HeLa and HCT116 cells expressing H2B-HaloTag and Fucci probes, we found that local nucleosome motion remained similar on average throughout interphase, except for elevated motion in early G1. Transcription inhibition similarly increased nucleosome motion throughout interphase. Local nucleosome motion also increased following replication stress or DNA damage. ConclusionOur findings suggest that near-constant chromatin motion supports housekeeping functions under similar physical conditions during interphase. Our findings also suggest that cells can transiently change chromatin motion to perform ad hoc tasks in response to signals from inside and outside the cell, such as DNA damage.

cell biology↗

bioRxiv2025

LRBA promotes drug-induced liver injury and MASLD by scaffolding MAPK activation

LPS-responsive beige-like anchor protein (LRBA) regulates vesicular trafficking and receptor recycling, and its deficiency results in immunodeficiency characterized by hypogammaglobulinemia and autoimmune syndrome. However, its role in liver pathophysiology remains unclear. Here, we reveal a previously unrecognized function of LRBA as a critical intracellular scaffold for mitogen-activated protein kinase (MAPK) activation that promotes liver injury. Lrba-/-mice exhibit reduced acetaminophen (APAP)-induced hepatic necrosis through the suppression of JNK activation. In a model of metabolic dysfunction-associated steatotic liver disease (MASLD) induced by a high-fat, high-cholesterol (HFHC) diet, Lrba deficiency reduces hepatic inflammation, fibrosis, and Kupffer cell activation. Mechanistically, LRBA homodimers directly interact with specific mitogen-activated protein kinase kinase kinases (MAP3Ks), including transforming growth factor-{beta}-activated kinase 1 (TAK1) and mixed-lineage kinase 3 (MLK3), to facilitate their activation. LRBA, which is primarily expressed in hepatocytes under physiological conditions, is upregulated in non-parenchymal cells such as Kupffer cells and cholangiocytes in both HFHC diet-fed mice and patients with MASLD and cirrhosis, linking its scaffolding function to pathological inflammation. Thus, LRBA promotes liver disease progression by amplifying inflammatory signaling.

cell biology↗

bioRxiv2025

Parasitism-mediated horizontal transfer of a functional cytochrome P450 gene entails transposon colonization in newly gained introns

Plants produce a wide variety of specialized metabolites that are typically present only in specific lineages. However, some specialized metabolites are found sporadically across distantly related plant species. While the latter cases have been explained as outcomes of convergent evolution, the molecular mechanism behind such metabolic evolution has remained largely elusive. Here, we report that parasitic dodders belonging to the genus Cuscuta accumulate sesamin, and that this accumulation may be attributed to the acquisition of enzymatically active homologs of Sesamum indicum CYP81Q1, which encodes piperitol/sesamin synthase (PSS). Phylogenetic analysis of CYP81Q homologs in Cuscuta and Grammica subgenera supports a trajectory in which ancestral Cuscuta species acquired CYP81Q from an ancestral host plant of Lamiales through horizontal gene transfer (HGT), and that the gene has been maintained during the speciation of Cuscuta. The evolution of the CYP81Q genes was accompanied by sequential intron gains, which likely involved the colonization of transposons. Experiments involving C. campestris and S. indicum suggested that expression of the host CYP81Q gene could be induced by parasitism, and physical connection to the host plant allowed the transfer of genetic elements to Cuscuta. These data suggest that parasitism-mediated HGT contributed to the transfer of a gene encoding a key enzyme in specialized lignan metabolism to Cuscuta, and that the acquired metabolic gene underwent structural modification while retaining its enzymatic function in dodders.

plant biology↗

bioRxiv2025

Intraspecific differences in habitat depth in a deep-sea isopod, Bathynomus doederleini (Crustacea: Isopoda: Cirolanidae), off the west coast of Kyushu, Japan

The giant deep-sea isopod, Bathynomus doederleini, is a benthic scavenger distributed in the northwestern Pacific. Despite its ecological importance, little is known about its habitat use and intraspecific variation in body size in relation to depth. In this study, we examined the habitat depth, size structure, and distributional limits of B. doederleini off the western coast of Kyushu, Japan, using baited traps deployed at depths ranging from 151 to 821 m. A total of 1,152 individuals were collected, with the highest catch per unit effort (CPUE) observed between 300 and 500 m. CPUE declined sharply below 700 m, likely due to thermal constraints and interspecific competition. Body size distribution varied significantly with depth: minimum body size increased with depth, while maximum body size remained constant. Smaller individuals were more abundant in shallower, warmer waters, suggesting ontogenetic habitat segregation possibly driven by metabolic and competitive factors. No brooding individuals were captured, supporting previous findings that reproductive females avoid baited traps. These results suggest that B. doederleini forms a reproductively active population in the East China Sea, with ecological adaptations to thermal conditions and depth-related niche partitioning. This study highlights the importance of trap type and environmental gradients in understanding deep-sea species ecology.

ecology↗

bioRxiv2025

Genetic diversity shapes behavioral outcomes and reveals sex differences in mice exposed to early life stress

Understanding how genetic variability shapes responses to environmental and developmental factors is critical for advancing translational neuroscience. However, most preclinical studies rely on inbred mouse strains that do not capture the genetic complexity of human populations. One key area of translational research focuses on identifying the neural and behavioral consequences of early life trauma. Rodent models of childhood neglect, such as maternal separation with early weaning (MSEW), have been used in isogenic mouse strains like C57BL/6J (B6) to identify behavioral domains and neural loci of deficits stemming from exposure to MSEW. To understand how genetic diversity may contribute to the outcomes produced by MSEW, and thus inform future studies on the topic, we utilized the Jackson Laboratory Diversity Outbred (DO) line, a population derived from eight founder strains that exhibit broad genetic and phenotypic heterogeneity. We first compared MSEW effects on social behavior in DO mice versus B6 mice, because we have previously found social behavior deficits in B6 mice with a history of MSEW. Indeed, we established that MSEW incited social motivation deficits in DO mice, in a sex-specific manner. We then expanded our investigation of DO mice to test MSEW-related changes in anxiety-like behavior, fear learning and expression, and reward-seeking. Results revealed that MSEW produces distinct, sex-specific phenotypes: female DO mice displayed reduced social motivation and elevated anxiety-like behavior, while male DO mice showed attenuated CS-evoked fear expression and diminished reward-seeking behavior. Additionally, immunohistochemical analysis revealed increased Fos expression in the paraventricular nucleus of the hypothalamus (PVN) in MSEW-exposed DO mice, both at baseline and following acute stress. These findings highlight the importance of incorporating genetically diverse models to better capture the nuances of early life adversity-related outcomes relevant to human populations.

neuroscience↗

bioRxiv2025

Engineering a Controlled Cardiac Multilineage Co-Differentiation Process Using Statistical Design of Experiments

BackgroundThe heart is a complex organ composed of diverse cell types, whose interplay is crucial for development, tissue homeostasis, and disease progression. A potential approach to recapitulate this heterotypic multicellular environment is the co-differentiation of induced pluripotent stem cells (iPSCs) into multiple cardiac cell types, facilitating the unlocking of their full potential for regenerative medicine and drug development. However, the inherent complexity of co-differentiation, where multiple differentiation factors simultaneously influence the induction of multiple cell types, presents a significant challenge in achieving high controllability over the process toward the desired outcome. Thus, a robust strategy is essential for engineering a controlled co-differentiation process with broader applicability. MethodsGiven the importance of heterotypic cellular proportions in facilitating proper interactions, we present a new strategy to engineer a controlled cardiac co-differentiation process from iPSCs using statistical design of experiments to simultaneously generate cardiomyocytes, mural cells, and endothelial cells, which are major constituents of the heart. ResultsWe divided the process into two stages: progenitor cell induction and the subsequent trilineage co-differentiation, allowing for stage-specific optimization. Given that the performance of progenitor cell induction may critically influence the overall process performance, we carefully optimized activin A and CHIR-99021 using the sequential design of experiments to achieve approximately 95% induction efficiency of KDR+/PDGFR-+ cardiogenic mesoderm cells from iPSCs with minimal batch-to-batch variability. In the trilineage co-differentiation stage, we developed unique multi-response models to delineate trilineage co-differentiation ratios within a defined parameter space of WNT signal inhibitor and vascular endothelial growth factor. This enabled the identification of potential conditions that steer co-differentiation toward desired cellular constitutions, a critical factor of effective cellular interplays. Repeated trilineage co-differentiation experiments confirmed the high process controllability, with a close match between actual and predicted differentiation ratios. Furthermore, cardiomyocytes from trilineage co-differentiation exhibited a more mature sarcomere gene expression profile than those from monolineage differentiation. ConclusionsThese results highlight the effectiveness of our strategy for engineering a stem cell co-differentiation process and its applicability where multicellular interactions are crucial.

bioengineering↗

bioRxiv2025

Floating offshore wind farms cause Japanese horse mackerel to congregate

Floating offshore wind farms (F-OWFs) are becoming key components of renewable energy production, yet their ecological impacts on marine ecosystems remain largely unexplored. Using environmental DNA (eDNA) analysis in the East China Sea, this study investigated the tendency for Japanese horse mackerel (Trachurus japonicus) to congregate beneath F-OWFs. Water samples were collected at stations near an F-OWF and control stations farther away at various depths and seasons. A total of 115 samples were analyzed, and eDNA of T. japonicus was detected in 83% of all samples. eDNA concentrations were significantly higher near an F-OWF (F-OWF stations) than at control stations. The highest recorded eDNA concentration reached 2,280 copies/L at an F-OWF station, whereas the maximum concentration at control stations was 783 copies/L. Seasonal variations were also observed, with lower concentrations in summer and higher concentrations from autumn to spring. Generalized linear model (GLM) analysis further revealed that wind turbines had a significant influence on eDNA concentration, whereas other environmental variables, such as water temperature and depth, were not significant. These findings suggest that F-OWFs may function as artificial reefs, providing habitat for commercially important fish and influencing fish distributions at both spatial and temporal scales. However, potential conflicts with fisheries due to spatial restrictions, displacement of fishery resources, and increased navigation costs necessitate further long-term ecological and socio-economic assessments. Integrating eDNA monitoring with traditional survey methods, such as acoustic surveys and ROV observations, is crucial for coexistence of adaptive offshore wind farm management and sustainable fisheries. Future research should also explore the long-term effects of F-OWFs on fish assemblages and biodiversity to support evidence-based decision-making for offshore energy development.

ecology↗

bioRxiv2025

The retinoic acid receptor regulates development of a key evolutionary novelty - the molluscan shell

The shells of molluscs are iconic structures of invertebrate exoskeletons supporting and protecting their soft body parts. The shell matrix molecules are synthesized and secreted from a shell-producing tissue, the shell gland. Shell gland cells develop at the early trochophore stage of the larvae. To date, the molecular signalling pathways by which the shell gland forms and starts to secrete the shell remains elusive. Here we demonstrate in the Pacific oyster Crassostrea gigas and the limpet Nipponacmea fuscoviridis, that the retinoic acid receptor (RAR), is crucial for inducing shell gland formation. RAR is expressed in both species in the shell gland at the late gastrula to early trochophore stages prior to the first production of shell. Suppression of the RAR by chemical inhibitors or gene-knock-down lead to a complete loss of the larval shell. Transcriptomic and in situ hybridisation analyses revealed that the developmental regulatory genes that are normally expressed in the shell gland, including engrailed, are down-regulated in the RAR-suppressed embryos. Using the RAR functional assay carried out on zebrafish embryos, we also revealed that the oyster RAR cannot transduce the RA signal in zebrafish, indicating that the molluscan RAR is clearly different from vertebrate RARs in its binding capacity to the RA. Our finding represents a key example of adaptive evolution of developmental "toolkit" genes for the origin of a major novel trait, the molluscan shell, in animals.

developmental biology↗

bioRxiv2024

Global identification of AGO3-RNA interactions in Chlamydomonas reveals the small RNA-mediated regulation of nuclear and chloroplast gene expression

MicroRNAs (miRNAs) form complexes with Argonaute (AGO) proteins and bind to mRNAs with complementary sequences to repress their expression. Organisms typically possess several hundred miRNAs regulating diverse biological processes. Although the roles of miRNAs have been well elucidated in multicellular organisms, they remain largely unexplored in unicellular organisms. In the green alga Chlamydomonas reinhardtii, the first unicellular organism in which miRNAs were discovered, identifying miRNA target genes remains challenging. Here, we report the high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to generate global AGO3-RNA interaction maps, identifying 131 mRNAs derived from nuclear genes. We also detected mRNAs from two chloroplast genes, suggesting that AGO3 may also influence chloroplast gene expression. Our findings indicate that Chlamydomonas small RNAs repress nuclear and chloroplast gene expression. Furthermore, HITS-CLIP analyses are now feasible for any RNA-binding protein in Chlamydomonas, offering new opportunities to uncover the functions of RNA-binding proteins of interest.

plant biology↗

bioRxiv2024

Brachiopod genome unveils the evolution of the BMP-Chordin network in bilaterian body patterning

Bone morphogenetic protein (BMP) signalling is crucial in regulating dorsal-ventral patterning and cell fate determination during early development in bilaterians. Interactions between BMP ligands and their main antagonist, Chordin, establish BMP gradients, subdivide embryos into distinct territories and organise body plans. However, the molecular control and evolutionary origins of dorsal-ventral patterning within spiralians, one of the three major bilaterian groups, have been obscured by their unique embryonic development. Here we present the chromosome-level genome of a spiralian with deuterostome-like development, the brachiopod Lingula anatina, and apply functional transcriptomics to study dorsal-ventral patterning under the control of BMP signalling. We uncover the presence of a dorsal-ventral BMP signalling gradient in the L. anatina gastrula with bmp2/4 and chordin expressed at its dorsal and ventral sides, respectively. Using small-molecule drugs, exogenous recombinant BMP proteins and RNA sequencing, we show that a high level of BMP pathway activation inhibits the expression of neural genes during gastrula and larval stages. We also show that BMP signalling splits the developing larval shell field into two valves. The discovery of a BMP-mediated dorsal-ventral patterning system in a spiralian, similar to those observed in deuterostomes and non-spiralian protostomes, suggests deep conservation of this mechanism across all three major bilaterian clades. This is further supported by striking similarities in the gene sets regulated by BMP signalling in brachiopods and the vertebrate model Xenopus. We argue that the spiralian ancestor retained the basal bilaterian mechanism of dorsal-ventral patterning, although downstream components of the BMP-Chordin network have undergone dynamic evolutionary changes.

evolutionary biology↗

bioRxiv2024

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

bioRxiv2024

Characterization of severe fever with thrombocytopenia syndrome virus Japanese isolate YG1 strain quasispecies using reverse genetics approaches

Three amino acid mutations have been identified in the isolated YG1 strain of severe fever thrombocytopenia syndrome virus (SFTSV), Gn (Y328H) accounts for 26.9% of the virus in patients blood, Gc (R624W) and L (N1891K) those are minor. To investigate viral properties caused by each mutation, we rescued viruses with one-three mutations. Mutations Y328H and R624W in GP increased the cell fusion activity and plaque size. Theses enhancement was more pronounced for both Y328H and R624W. The pseudotyped vesicular stomatitis virus coated with the SFTSV GP Y328H mutant showed lower infectivity in Vero E6 cells, which was compensated for by the additional R624W mutation. In the process of adaptation for virus with Y328H, the R624W mutation may be acquired. Moreover, only the viruses with the N1891K mutation in L showed significant CPE and the CPE was inhibited by the pan-caspase inhibitor, suggesting that caspase-dependent cell death occurred. Programmed cell death associated molecules caspase-1 and caspase-3 were induced in both CPE inducing and wild-type virus-infected cells. Furthermore, infection with the wild-type virus suppressed actinomycin D-induced cell death. These results suggest that SFTSV infected cells initiate programmed cell death, whereas wildt-ype virus may inhibit cell death. Furthermore, the N1891K mutation in L virus was outcompeted by a 10-fold less wild-type virus in Vero E6 cells indicating that it was not advantageous for viral survival in Vero E6 cells. Thus the quasispecies composition of SFTSV appeared to be influenced by propagative environment. ImportanceThis study shows information on viral pathogenesis by analyzing quasispecies derived from one fatal case of severe fever with thrombocytopenia syndrome virus (SFTSV) infection. Observation with recombinant SFTSV altered Gn and Gc suggests that combining mutations may increase the viability of mutant viruses, selecting viruses to create a suitable population for propagation. The N1891K mutation in L protein of SFTSV was related to CPE appearance. On the other hand, wild-type virus which is major population in patient infection was suppressive for cell death. It was suggested that SFTSV has a mechanism to escape cell death for the prolonged viral propagation in infected cells. Although the mechanism is still unknown, it has been suggested that RNA virus polymerase might be involved in the regulation of cell death. This study proposed the mechanism underlying the adaptation to the environment and survival of virus as quasispecies.

microbiology↗

bioRxiv2024

Nobiletin, a Polymethoxyflavonoid, Activates the Desuccinylase Activity of SIRT5 and Prevents the Development of Heart Failure

Nobiletin is a natural compound useful for the prevention and treatment of several diseases. However, the precise role of nobiletin in heart failure is unclear. Nobiletin treatment prevents pressure overload- and myocardial infarction-induced heart failure. Using affinity purification of biotinylated nobiletin from rat heart cell lysates, we identified sirtuin 5 (SIRT5) as a novel nobiletin-binding protein. Nobiletin enhanced the desuccinylase activity of SIRT5 in vitro. Compared to wild-type mice, SIRT5-overexpressing transgenic mice resisted pressure overload-induced systolic dysfunction. Conversely, SIRT5 knockout disrupted the nobiletin-mediated therapeutic effects on heart failure in mice. SIRT5 desuccinylated p300 at lysine 1568 and reduced the histone acetyltransferase (HAT) activity of p300. The desuccinylated p300 mutant suppressed the phenylephrine-induced cardiomyocyte hypertrophic responses. These findings suggest that nobiletin prevents heart failure development through SIRT5-dependent inhibition of p300-HAT activity. Nobiletin, a nontoxic dietary compound, is a potential therapeutic agent for heart failure in humans.

molecular biology↗

bioRxiv2024

De novo annotation of the wheat pangenome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

Wheat is the most widely cultivated crop in the world with over 215 million hectares grown annually. However, to meet the demands of a growing global population, breeders face the challenge of increasing wheat production by approximately 60% within the next 40 years. The 10+ Wheat Genomes Project recently sequenced and assembled to chromosome level the genomes of nine wheat cultivars to develop our understanding of genetic diversity and selection within the pan-genome of wheat. Here, we provide a wheat pan-transcriptome with de novo annotation and differential expression analysis for these wheat cultivars, across multiple different tissues and whole seedlings sampled at dusk/dawn. Analysis of these de novo annotations facilitated the discovery of genes absent from the Chinese Spring reference, identified genes specific to particular cultivars and defined the core and dispensable genomes. Expression analysis across cultivars and tissues revealed conservation in expression between a large core set of homeologous genes, but also widespread changes in subgenome homeolog expression bias between cultivars. Co-expression network analysis revealed the impact of divergence of sub-genome homeolog expression and identified cultivar-specific expression profiles. In a case study utilising both the newly constructed wheat pan-genome and pan-transcriptome we demonstrate prevalent variation in the prolamin superfamily and immune-reactive proteins across the pan-cultivars.In summary, this work provides both a valuable resource for the wider wheat community and reveals diversity in gene content and expression patterns between global wheat cultivars.

genomics↗

bioRxiv2023

Environmental DNA Reveals the Geographic Distributions of Two Eel Species, Anguilla japonica and A. marmorata, in Western Kyushu, Japan

Anguillid eels migrate thousands of kilometres from their spawning grounds, dispersing across a vast geographic area to fresh and brackish water habitats, where they settle and grow. Japanese eels (Anguilla japonica) and giant mottled eels (A. marmorata) are both found in Japan, although their distributions differ. However, details of these differences are unknown. We hypothesised that distribution patterns of Japanese and giant mottled eels must be different between and within rivers along the northwest coast of Kyushu, Japan. Environmental DNA (eDNA) analysis was conducted at 87 sites in 23 rivers. Japanese eel eDNA was detected in 19 rivers (82.6%) and that of giant mottled eels was detected in 8 (34.8%). eDNA for Japanese eels was detected at 6 of 9 sites in the North (66.7%), 13 of 23 sites in Omura (56.5%) and 37 of 55 sites in the South (67.3%). In contrast, giant mottled eel eDNA was detected at 1 of 9 sites in the North (11.1%), no sites in Omura and 15 of 55 sites in the South (27.3%). There was no correlation between eDNA concentrations of the two species at 10 sites in the five rivers where eDNA of both species was detected, implying that their habitat preference differ. This partially reveals dispersal and settlement mechanisms of these eel species.

ecology↗