Biology subjects

Lee, H.-H.

Publications and source records attributed to Lee, H.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

Endogenous attention is invariant to sequential effects in performance around the visual field

Covert spatial attention selects and prioritizes relevant sensory information. Endogenous attention is voluntary, goal-driven, and flexible. However, it cannot alleviate visual polar-angle asymmetries, specifically, the horizontal-vertical anisotropy and the vertical meridian asymmetry. Visual perception is affected by both current sensory inputs and contextual information over time and space, such as the perception of preceding trials. Previous studies reported sequential effects whereby attention interacts with response repetitions. But it is unknown whether and how endogenous attention modulation on performance varies as a function of target location and trial history. Here, we reanalyzed data from three published studies of endogenous attention in orientation discrimination tasks, to (1) assess the typical sequential effects on response, in which response to the current trial is biased toward the previous one, and (2) examine if sequential effects would modulate the performance across locations, across four dimensions: (1) location, (2) feature, (3) attention repetition condition, and (4) the correctness of the preceding (n -1) trial. First, we demonstrated typical sequential effects of response repetition to the repeated location and feature aspects of the target. Second, we found a robust effect of attention on performance, but the results did not reveal evidence of sequential attention effects as a function of the four dimensions in any of the three studies. Moreover, there were no interactions between attention and location when considering trial history. Together, these findings provide compelling evidence that visual polar-angle asymmetries are resistant to endogenous attention, and that even top- down factors-sequential effects-do not alleviate these asymmetries in performance.

neuroscience↗

bioRxiv2026

Transcranial magnetic stimulation to frontal cortex, unlike occipital stimulation, does not disrupt exogenous attention

Orienting covert attention to a target location improves performance across a wide array of visual tasks [1, 2]. Whereas fMRI studies have identified partially overlapping frontoparietal networks underlying endogenous (voluntary) and exogenous (involuntary) covert attention, these correlational methods cannot establish whether a given region is functionally necessary. Prior neurostimulation studies have established that early visual cortex (V1/V2) is critical for exogenous [3, 4] but not endogenous attention [5], whereas the right frontal eye field (rFEF+) is critical for endogenous attention [5]. Here, we used a combined psychophysical-TMS protocol to investigate whether rFEF+ is also required for exogenous attention. Participants performed an orientation discrimination task, in which a peripheral cue (valid, neutral, or invalid) preceded a target and a distractor stimulus. We applied two successive TMS pulses to rFEF+ during stimulus presentation and measured contrast-response functions (CRFs) to quantify perceptual sensitivity (d') across all attention cueing and stimulation conditions. When the distractor was stimulated, exogenous attention yielded a characteristic response gain at the target--with performance benefits for valid cues and costs for invalid cues at high contrast levels. Crucially, this response gain was entirely preserved when the target was stimulated. This pattern contrasts with previous findings demonstrating that TMS to V1/V2 eliminates exogenous attentional effects at the stimulated location. These results indicate that rFEF+ is not necessary for exogenous attention, and together with previous studies [3-5] complete a double dissociation: rFEF+ is critical for endogenous but not exogenous attention, whereas V1/V2 is critical for exogenous but not endogenous attention. These findings reveal a distinct causal cortical architecture for voluntary and involuntary spatial attention, suggesting that they rely on different cortical scaffolds.

neuroscience↗

bioRxiv2025

Polar angle asymmetries persist despite covert spatial attention and differential adaptation

Visual adaptation and attention are two processes that help manage the brains limited bioenergetic resources for perception. Visual perception is heterogeneous around the visual field: it is better along the horizontal than the vertical meridian (horizontal-vertical anisotropy, HVA), and better along the lower than the upper vertical meridian (vertical meridian asymmetry, VMA). Recently, we showed that visual adaptation is more pronounced at the horizontal than the vertical meridian, but whether and how this differential adaptation modulates the effects of covert spatial attention remains unknown. In this study, we investigated whether and how the effects of endogenous (voluntary) and exogenous (involuntary) covert attention on an orientation discrimination task vary at the cardinal meridians, with and without adaptation. We manipulated endogenous (Experiment 1) or exogenous (Experiment 2) attention via an informative central or uninformative peripheral cue, respectively. Results showed that (1) in the non-adapted condition, the typical HVA and VMA emerged in contrast thresholds; (2) the adaptation effect was stronger at the horizontal than the vertical meridian; and (3) regardless of adaptation, both endogenous and exogenous attention enhanced and impaired performance at the attended and unattended locations, respectively, to a similar degree at both cardinal meridians. Together, these findings reveal that, despite differences between endogenous and exogenous attention, their effects remain uniform across cardinal meridians-even under differential adaptation that reduces intrinsic asymmetries of visual field representations.

neuroscience↗

bioRxiv2025

Distinct cellular processes drive motor skill learning in the human brain

Despite decades of research, the biological mechanisms by which motor skills consolidate in the human brain remain poorly understood. Diffusion MRI provides a unique opportunity to probe biological processes non-invasively, as water displacements occur on the micrometer scale. Using diffusion tensor imaging (DTI), our team showed that motor sequence learning (MSL) induces microstructural changes in the hippocampus and key motor regions, suggesting that declarative and procedural systems may operate as part of the same network. Yet DTI cannot identify the cellular source of these changes, leaving open whether they reflect structural plasticity --remodeling of dendritic and astrocytic processes described in rodents-- or transient homeostatic responses that accompany learning --neuronal and astrocytic swelling. Here, we combined ultra-high-gradient diffusion MRI with the compartment-based Soma and Neurite Density Imaging (SANDI) model to disentangle the cellular basis of motor skill memory consolidation. DTI showed that MSL induced rapid microstructural changes in the hippocampus, precuneus, and motor regions, but only those in the precuneus and posterior parietal cortex (PPC) persisted overnight. SANDI revealed that DTI changes were driven by two distinct cellular processes: a transient enlargement of the cell soma across all regions consistent with a short-lived homeostatic response, and a sustained rise in cell-process density restricted to the precuneus and PPC, compatible with structural plasticity. By decomposing diffusion signals into their cellular sources, our work disambiguates transient and enduring processes, providing the first non-invasive evidence for the cellular basis of human motor memory consolidation and a framework for studying neuroplasticity in vivo.

neuroscience↗

bioRxiv2025

Visual adaptation stronger at horizontal than vertical meridian: Linking performance with V1 cortical surface area

Visual adaptation reduces bioenergetic expenditure by decreasing sensitivity to repetitive and similar stimuli. In human adults, visual performance varies systematically around polar angle for many visual dimensions and tasks: Performance is superior along the horizontal than the vertical meridian (horizontal-vertical anisotropy, HVA), and the lower than upper vertical meridian (vertical meridian asymmetry, VMA). These asymmetries are resistant to spatial and temporal attention. However, it remains unknown whether visual adaptation differs around polar angle. Here, we investigated how adaptation influences contrast sensitivity at the fovea and perifovea across the four cardinal meridian locations, for both horizontal and vertical stimuli in an orientation discrimination task. In the non-adapted conditions, the HVA was more pronounced for horizontal than vertical stimuli. For both orientations, adaptation was stronger along the horizontal than vertical meridian, exceeding foveal adaptation. Additionally, perifoveal adaptation effects positively correlated with individual V1 cortical surface area. These findings reveal that visual adaptation mitigates the HVA in contrast sensitivity, fostering perceptual uniformity around the visual field while conserving bioenergetic resources.

neuroscience↗

bioRxiv2024

In vivo human neurite exchange imaging (NEXI) at 500 mT/m diffusion gradients

Evaluating tissue microstructure and membrane integrity in the living human brain through diffusion-water exchange imaging is challenging due to requirements for a high signal-to-noise ratio and short diffusion times dictated by relatively fast exchange processes. The goal of this work was to demonstrate the feasibility of in vivo imaging of tissue micro-geometries and water exchange within the brain gray matter using the state-of-the-art Connectome 2.0 scanner equipped with an ultra-high-performance gradient system (maximum gradient strength=500 mT/m, maximum slew rate=600 T/m/s). We performed diffusion MRI measurements in 15 healthy volunteers at multiple diffusion times (13-30 ms) and b-values up to 17.5 ms/m2. The anisotropic Karger model was applied to estimate the exchange time between intra-neurite and extracellular water in gray matter. The estimated exchange time across the cortical ribbon was around (median{+/-}interquartile range) 13{+/-}8 ms on Connectome 2.0, substantially faster than that measured using an imaging protocol compatible with Connectome 1.0-alike systems on the same cohort. Our investigation suggested that the NEXI exchange time estimation using a Connectome 1.0 compatible protocol was more prone to residual noise floor biases due to the small time-dependent signal contrasts across diffusion times when the exchange is fast ([≤]20 ms). Furthermore, spatial variation of exchange time was observed across the cortex, where the motor cortex, somatosensory cortex and visual cortex exhibit longer exchange times compared to other cortical regions. Non-linear fitting for the anisotropic Karger model was accelerated 100 times using a GPU-based pipeline compared to the conventional CPU-based approach. This study highlighted the importance of the chosen diffusion times and measures to address Rician noise in dMRI data, which can have a substantial impact on the estimated NEXI exchange time and require extra attention when comparing NEXI results between various hardware setups. Highlights- The Connectome 2.0 scanner equipped with 500 mT/m gradients enables high-sensitivity diffusion MRI for imaging exchange times in vivo - The global exchange time across the living human cortex was estimated to be about 13 ms on Connectome 2.0, faster than measured using a protocol compatible to Connectome 1.0 - Spatially varying exchange times were observed across the cortex - A GPU-accelerated tool was developed to speed up parameter estimation by 100 times - The narrow pulse approximation used in neurite exchange imaging does not affect estimation performance in high gradient performance MRI systems

neuroscience↗

bioRxiv2024

All-trans retinoic acid-mediated ADAR1 degradation synergizes with PD-1 blockade to suppress pancreatic cancer

As a double-stranded RNA-editing enzyme and an interferon-stimulated gene, double-stranded RNA-specific adenosine deaminase (ADAR1) suppresses interferon signaling and contributes to immunotherapy resistance. Suppression of ADAR1 overcomes immunotherapy resistance in preclinical models, but has not yet been translated to clinical settings. By conducting a screening of a subset of the FDA-approved drugs, we found that all-trans retinoic acid (ATRA, also known as tretinoin) caused ADAR1 protein degradation through ubiquitin-proteasome pathways and concomitantly increased PD-L1 expression in pancreatic and breast cancers. In addition, the combination of ATRA and PD-1 blockade reprogrammed the tumor microenvironment and unleashed antitumor immunity and thereby impeded tumor growth in pancreatic cancer mouse models. In a pilot clinical trial, a higher dose of ATRA plus the anti-PD-1 antibody nivolumab prolonged median overall survival in patients with chemotherapy-resistant pancreatic cancer compared to a lower dose of the same regimen. In this study, ATRA was the first drug to be found to cause ADAR1 degradation. We propose translation of a promising 2-pronged antitumor strategy using ATRA and nivolumab to convert immunologically "cold" into "hot" tumors susceptible to immune checkpoint blockade.

cancer biology↗

bioRxiv2024

Single cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy

Single cell RNA sequencing (scRNA-seq) has emerged as a versatile tool in biology, enabling comprehensive genomic-level characterization of individual cells. Currently, most scRNA-seq methods generate barcoded cDNAs by capturing polyA tails of mRNAs, which excludes many non-coding RNAs (ncRNAs), especially those transcribed by RNA polymerase III (Pol III). Although previously thought to be expressed constitutively, Pol III-transcribed ncRNAs are expressed variably in healthy and disease states and play important roles therein, necessitating their profiling at the single cell level. In this study, we have developed a measurement protocol for nc886 as a model case, as an initial step for scRNA-seq for Pol III-transcribed ncRNAs. Specifically, we spiked in an oligo-tagged nc886-specific primer during the polyA tail capture process for the 5-reading in scRNA-seq. We then produced sequencing libraries for standard 5 gene expression and oligo-tagged nc886 separately, to accommodate different cDNA sizes and ensure undisturbed transcriptome analysis. We applied this protocol in three cell lines which express high, low, and zero levels of nc886, respectively. Our results show that the identification of oligo tags exhibited limited target specificity, and sequencing reads of nc886 enabled the correction of non-specific priming. These findings suggest that gene-specific primers (GSPs) can be employed to capture RNAs lacking a polyA tail, with subsequent sequence verification ensuring accurate gene expression counting. Moreover, we embarked on an analysis of differentially expressed genes in cell line sub-clusters with differential nc886 expression, demonstrating variations in gene expression phenotypes. Collectively, the primer spike-in strategy allows us for a combined analysis of ncRNAs and gene expression phenotype.

genomics↗

bioRxiv2024

Romer-EPTI: Rotating-view motion-robust super-resolution EPTI for SNR-efficient distortion-free in-vivo mesoscale dMRI and microstructure imaging

PurposeTo overcome the major challenges in dMRI acquisition, including low SNR, distortion/blurring, and motion vulnerability. MethodsA novel Romer-EPTI technique is developed to provide distortion-free dMRI with significant SNR gain, high motion-robustness, sharp spatial resolution, and simultaneous multi-TE imaging. It introduces a ROtating-view Motion-robust supEr-Resolution technique (Romer) combined with a distortion/blurring-free EPTI encoding. Romer enhances SNR by a simultaneous multi-thick-slice acquisition with rotating-view encoding, while providing high motion-robustness through a motion-aware super-resolution reconstruction, which also incorporates slice-profile and real-value diffusion, to resolve high-isotropic-resolution volumes. The in-plane encoding is performed using distortion/blurring-free EPTI, which further improves effective spatial resolution and motion robustness by preventing not only T2/T2*-blurring but also additional blurring resulting from combining encoded volumes with inconsistent geometries caused by dynamic distortions. Self-navigation was incorporated to enable efficient phase correction. Additional developments include strategies to address slab-boundary artifacts, achieve minimal TE for SNR gain at 7T, and achieve high robustness to strong phase variations at high b-values. ResultsUsing Romer-EPTI, we demonstrate distortion-free whole-brain mesoscale in-vivo dMRI at both 3T (500-m-iso) and 7T (485-m-iso) for the first time, with high SNR efficiency (e.g., [Formula]), and high image quality free from distortion and slab-boundary artifacts with minimal blurring. Motion experiments demonstrate Romer-EPTIs high motion-robustness and ability to recover sharp images in the presence of motion. Romer-EPTI also demonstrates significant SNR gain and robustness in high b-value (b=5000s/mm2) and time-dependent dMRI. ConclusionRomer-EPTI significantly improves SNR, motion-robustness, and image quality, providing a highly efficient acquisition for high-resolution dMRI and microstructure imaging.

bioengineering↗

bioRxiv2023

Adaptation and exogenous attention interact in the early visual cortex: A TMS study

Transcranial magnetic stimulation (TMS) to early visual cortex modulates the effect of adaptation and eliminates the effect of exogenous (involuntary) attention on contrast sensitivity. Here we investigated whether adaptation modulates exogenous attention under TMS to V1/V2. Observers performed an orientation discrimination task while attending to one of two stimuli, with or without adaptation. Following an attentional cue, two stimuli were presented in the stimulated region and its contralateral symmetric region. A response cue indicated the stimulus whose orientation observers had to discriminate. Without adaptation, in the distractor-stimulated condition, contrast sensitivity increased at the attended location and decreased at the unattended location via response gain-but these effects were eliminated in the target-stimulated condition. Critically, after adaptation, exogenous attention altered performance similarly in both distractor-stimulated and target-stimulated conditions. These results reveal that (1) adaptation and attention interact in the early visual cortex, and (2) adaptation shields exogenous attention from TMS effects.

neuroscience↗

bioRxiv2023

In vivo Mapping of Cellular Resolution Neuropathology in Brain Ischemia by Diffusion MRI

Non-invasive mapping of cellular pathology can provide critical diagnostic and prognostic information. Recent developments in diffusion MRI have produced new tools for examining tissue microstructure at a level well below the imaging resolution. Here, we report the use of diffusion time (t)-dependent diffusion kurtosis imaging (tDKI) to simultaneously assess the morphology and transmembrane permeability of cells and their processes in the context of pathological changes in hypoxic-ischemic brain (HI) injury. Through Monte Carlo simulations and cell culture organoid imaging, we demonstrate feasibility in measuring effective size and permeability changes based on the peak and tail of tDKI curves. In a mouse model of HI, in vivo imaging at 11.7T detects a marked shift of the tDKI peak to longer t in brain edema, suggesting swelling and beading associated with the astrocytic processes and neuronal neurites. Furthermore, we observed a faster decrease of the tDKI tail in injured brain regions, reflecting increased membrane permeability that was associated with upregulated water exchange upon astrocyte activation at acute stage as well as necrosis with disrupted membrane integrity at subacute stage. Such information, unavailable with conventional diffusion MRI at a single t, can predict salvageable tissues. For a proof-of-concept, tDKI at 3T on an ischemic stroke patient suggested increased membrane permeability in the stroke region. This work therefore demonstrates the potential of tDKI for in vivo detection of the pathological changes in microstructural morphology and transmembrane permeability after ischemic injury using a clinically translatable protocol.

bioengineering↗

bioRxiv2023

The influence of axonal beading and undulation on axonal diameter mapping

We consider the effect of non-cylindrical axonal shape on axonal diameter mapping with diffusion MRI. Practical sensitivity to axon diameter is attained at strong diffusion weightings b, where the deviation from the [Formula] scaling yields the finite transverse diffusivity, which is then translated into axon diameter. While axons are usually modeled as perfectly straight, impermeable cylinders, the local variations in diameter (caliber variation or beading) and direction (undulation) have been observed in microscopy data of human axons. Here we quantify the influence of cellular-level features such as caliber variation and undulation on axon diameter estimation. For that, we simulate the diffusion MRI signal in realistic axons segmented from 3-dimensional electron microscopy of a human brain sample. We then create artificial fibers with the same features and tune the amplitude of their caliber variations and undulations. Numerical simulations of diffusion in fibers with such tunable features show that caliber variations and undulations result in under- and over-estimation of axon diameters, correspondingly; this bias can be as large as 100%. Given that increased axonal beading and undulations have been observed in pathological tissues, such as traumatic brain injury and ischemia, the interpretation of axon diameter alterations in pathology may be significantly confounded.

neuroscience↗

bioRxiv2023

Single worm long read sequencing reveals genome diversity in free-living nematodes

Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from Dorylaimia, Enoplia, and early-branching species in Chromadoria. These free-living species had larger genome sizes, ranging from 147-792 Mb, compared to those of the parasitic lifestyle. Nine mitogenomes were fully assembled and displaying a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.

genomics↗

bioRxiv2023

Eddy current-induced artifacts correction in high gradient strength diffusion MRI with dynamic field monitoring: demonstration in ex vivo human brain imaging

PurposeTo demonstrate the advantages of spatiotemporal magnetic field monitoring to correct eddy current-induced artifacts (ghosting and geometric distortions) in high gradient strength diffusion MRI (dMRI). MethodsA dynamic field camera with 16 NMR field probes was used to characterize eddy current fields induced from diffusion gradients for different gradients strengths (up to 300 mT/m), diffusion directions, and shots in a 3D multi-shot EPI sequence on a 3T Connectom scanner. The efficacy of dynamic field monitoring-based image reconstruction was demonstrated on high-resolution whole brain ex vivo dMRI. A 3D multi-shot image reconstruction framework was informed with the actual nonlinear phase evolution measured with the dynamic field camera, thereby accounting for high-order eddy currents fields on top of the image encoding gradients in the image formation model. ResultsEddy current fields from diffusion gradients at high gradient strength in a 3T Connectom scanner are highly nonlinear in space and time, inducing high-order spatial phase modulations between odd/even echoes and shots that are not static during the readout. Superior reduction of ghosting and geometric distortion was achieved with dynamic field monitoring compared to ghosting approaches such as navigator- and structured low-rank-based methods or MUSE, followed by image-based distortion correction with eddy. Improved dMRI analysis is demonstrated with diffusion tensor imaging and high-angular resolution diffusion imaging. ConclusionStrong eddy current artifacts characteristic of high gradient strength dMRI can be well corrected with dynamic field monitoring-based image reconstruction, unlike the two-step approach consisting of ghosting correction followed by geometric distortion reduction with eddy.

bioengineering↗

bioRxiv2022

The Aphelenchoides genomes reveal major events of horizontal gene transfers in clade IV nematodes

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are amongst the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of horizontal gene transfer in nematodes.

genomics↗

bioRxiv2022

Enhanced expression of 4-Cl-IAA and 6-Cl-IAA by touch stimulus for rapid and differential growths of the Madeira vine

Madeira vine (MV) grows 30 times faster after encountering a support. In vivo x-ray diffraction made on live MV stems revel the appearance of crystallized IAA (C10H9NO2), 4-Cl-IAA (C10H8ClNO2) and 6-Cl-IAA (C10H8ClNO2) in the stems. Small angle neutron scattering spectra of the IAA extracted from MVs stem reveal a progressive increase in the size of crystallized IAA transported downward from the apex of the shoots. High resolution X-ray diffractions made on the extracted IAA reveal significantly larger amounts of 4-Cl-IAA and 6-Cl-IAA in the climbing MVs than in the swaying around MVs. The gas chromatography-mass spectrometry spectra reveal the production of 9% more IAA and 90% more 4-Cl-IAA+6-Cl-IAA at the apexes of climbing MVs than swaying MVs. More 4-Cl-IAA+6-Cl-IAA were transported to the contact-free side than to the contact side of the vine. In vivo neutron tomography of naturally climbing MVs reveals a substantially higher H+ concentration in the contact-free parts than in the contact parts. The absorption spectra also reveal more expansin in the contact-free parts than in the contact parts. These results provide a view, at the molecular level, of what triggers the faster and differential growths in MVs in response to touching a support.

plant biology↗

bioRxiv2022

Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitochondrial genomes from sampling to annotation using existing protocols and programs. Approximately 4Gb of sequence was produced from 15 Flongle and two R9.4 Flowcells, averaging 235Mb and N50=4.4kb per Flowcell. Five of the six 14.1-18kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing reveal that the ONT assemblies were able to span over highly AT rich sequence in the control region that was otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7bp with the majority occurring at homopolymer regions. Our findings suggest that ONT are portable and can be used to rapidly produce mitogenomes at low cost and tailored to genomics-based training in biodiversity research.

ecology↗

bioRxiv2022

Fusarium solani species complex genomes reveal bases of compartmentalisation and animal pathogenesis

The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced and compared six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins and revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). Each chromosome type varied in structural architectures, with FC and LS chromosomes containing significantly higher proportions of repetitive elements and methylation levels than core chromosomes, with genes exhibiting higher dN/dS and enriched in functions related to pathogenicity and niche expansion. Mesosynteny were detected between FC chromosomes of Fusarium genomes, indicating that these chromosomes were present in a common ancestor that predated FSSC species. These findings provide evidence that genome compartmentalisation was the outcome of multi-speed evolution amongst FSSC chromosomes. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating Pelodiscus sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. The study establishes genomic resources and an animal model for fungal pathogens of trans-kingdom hosts.

genomics↗