Biology subjects

Lee, J. T.

Publications and source records attributed to Lee, J. T..

17 recordsLinked to original sources

bioRxiv2025

Antiviral and anti-inflammatory effects of Tabamide A derivative, TA25, against human rhinovirus and multiple zoonotic viruses in vitro and in silico

Human rhinovirus (HRV), first isolated in 1956, belongs to the family Piconaviridae containing a positive-sense, single-stranded RNA genome. HRV causes mild cold and severe respiratory disease, such as asthma, COPD, and pneumonia. To date, no Food and Drug Administration-approved antiviral or anti-inflammatory drugs are available for HRV. TA25 is a phenolic amide derivative extracted from the leaves of Nicotiana tabacum. To investigate the potential candidate for antiviral therapeutics against zoonotic viruses, we evaluated the antiviral potency of TA25 for HRV and multiple zoonotic viruses. The antiviral and anti-inflammatory effects of TA25 were evaluated using RT-qPCR and RNA-seq. Strand-specific RT-qPCR was performed to measure genomic and anti-genomic RNA expression after TA25 treatment. In addition, an AI-based docking test was conducted to investigate the binding affinity of TA25 with viral target proteins. TA25 induced a significant reduction in viral replication and suppressed the expression of pro-inflammatory genes. Inhibition of viral replication by TA25 treatment was confirmed by strand-specific RT-qPCR. TA25 showed broad-spectrum antiviral activity against multiple viruses, including HRV-1A, Zika virus, Dengue virus, Vaccinia virus, and Influenza B virus Victoria. Using an AI-driven structure-based docking analysis, TA25 showed the strongest binding affinity with the HRV 2B protein. This study demonstrates that TA25 confers the broad antiviral and anti-inflammatory activity against HRV and multiple zoonotic viruses. These findings provide valuable insights into antiviral strategies of TA25 for a promising therapeutic candidate in response to emerging RNA and DNA viruses.

microbiology↗

bioRxiv2024

Dosage compensation of transposable elements in mammals

In mammals, X-linked dosage compensation involves two processes: X-chromosome inactivation (XCI) to balance X chromosome dosage between males and females, and hyperactivation of the remaining X chromosome (Xa-hyperactivation) to achieve X-autosome balance in both sexes. Studies of both processes have largely focused on coding genes and have not accounted for transposable elements (TEs) which comprise 50% of the X-chromosome, despite TEs being suspected to have numerous epigenetic functions. This oversight is due in part to the technical challenge of capturing repeat RNAs, bioinformatically aligning them, and determining allelic origin. To overcome these challenges, here we develop a new bioinformatic pipeline tailored to repetitive elements with capability for allelic discrimination. We then apply the pipeline to our recent So-Smart-Seq analysis of single embryos to comprehensively interrogate whether X-linked TEs are subject to either XCI or Xa-hyperactivation. With regards to XCI, we observe significant differences in TE silencing in parentally driven "imprinted" XCI versus zygotically driven "random" XCI. Chromosomal positioning and genetic background impact TE silencing. We also find that SINEs may influence 3D organization during XCI. In contrast, TEs do not undergo Xa-hyperactivation. Thus, while coding genes are subject to both forms of dosage compensation, TEs participate only in Xi silencing. Evolutionary and functional implications are discussed.

genetics↗

bioRxiv2024

Cleavage region organizes the structural architecture of the B2 SINE ribozyme

The SINE-encoded B2 retrotransposon is an RNA Polymerase III transcript that gets upregulated during various cellular stress responses. The B2 noncoding RNA can directly inhibit RNA Polymerase II, leading to a significant downregulation of transcripts during stress. Our recent findings have shown that B2 is a self-cleaving epigenetic ribozyme and that cleavage can be induced by interactions with epigenetic factors, co-regulating its function across distinct chromatin-binding target loci. Here, by integrating RNA chemical probing, small angle X-ray scattering, and 3D motif modeling, we determine structural ensemble-to-function relations for the B2 SINE ribozyme RNA. Perturbations of the RNA suggest that the B2 SINE ribozyme has a well-defined secondary structure and dynamic tertiary structure that both critically depend on the presence of the active site of cleavage. In an RNA engineering approach, we examine the effect of point mutations, deletions of the main cleavage site and deletions of the cleavage domain on the structural ensemble of the RNA. By combining this with functional data, we obtain relations of structural ensembles to various functional states. This perturbative approach serves as a template to unravel the relation of structural ensembles to functional states for other ncRNA and mRNA systems.

biophysics↗

bioRxiv2024

Xist RNA binds select autosomal genes and depends on Repeat B to regulate their expression

Xist, a pivotal player in X chromosome inactivation (XCI), has long been perceived as a cis-acting long noncoding RNA that binds exclusively to the inactive X chromosome (Xi). However, Xists ability to diffuse under select circumstances has also been documented, leading us to suspect that Xist RNA may have targets and functions beyond the Xi. Here, using female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as models, we demonstrate that Xist RNA indeed can localize beyond the Xi. However, its binding is limited to [~]100 genes in cells undergoing XCI (ES cells) and in post-XCI cells (MEFs). The target genes are diverse in function but are unified by their active chromatin status. Xist binds discretely to promoters of target genes in neighborhoods relatively depleted for Polycomb marks, contrasting with the broad, Polycomb-enriched domains reported for human XIST RNA. We find that Xist binding is associated with down-modulation of autosomal gene expression. However, unlike on the Xi, Xist binding does not lead to full silencing and also does not spread beyond the target gene. Over-expressing Xist in transgenic ES cells similarly leads to autosomal gene suppression, while deleting Xists Repeat B motif reduces autosomal binding and perturbs autosomal down-regulation. Furthermore, treating female ES cells with the Xist inhibitor, X1, leads to loss of autosomal suppression. Altogether, our findings reveal that Xist targets [~]100 genes beyond the Xi, identify Repeat B as a crucial domain for its in-trans function in mice, and indicate that autosomal targeting can be disrupted by a small molecule inhibitor.

genomics↗

bioRxiv2023

A therapeutic small molecule lead enhances γ-oscillations and improves cognition/memory in Alzheimer's disease model mice

Brain rhythms provide the timing and concurrence of brain activity required for linking together neuronal ensembles engaged in specific tasks. In particular, the {gamma}-oscillations (30-120 Hz) orchestrate neuronal circuits underlying cognitive processes and working memory. These oscillations are reduced in numerous neurological and psychiatric disorders, including early cognitive decline in Alzheimers disease (AD). Here we report on a potent brain permeable small molecule, DDL-920 that increases {gamma}-oscillations and improves cognition/memory in a mouse model of AD, thus showing promise as a new class of therapeutics for AD. As a first in CNS pharmacotherapy, our lead candidate acts as a potent, efficacious, and selective negative allosteric modulator (NAM) of the {gamma}-aminobutyric acid type A receptors (GABAARs) assembled from 1{beta}2{delta} subunits. We identified these receptors through anatomical and pharmacological means to mediate the tonic inhibition of parvalbumin (PV) expressing interneurons (PV+INs) critically involved in the generation of {gamma}-oscillations. Our approach is unique as it is meant to enhance cognitive performance and working memory in a state-dependent manner by engaging and amplifying the brains endogenous {gamma}-oscillations through enhancing the function of PV+INs.

neuroscience↗

bioRxiv2023

Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato

Lyme disease (LD), caused by spirochete bacteria of the genus Borrelia burgdorferi sensu lato, remains the most common vector-borne disease in the northern hemisphere. Borrelia outer surface protein A (OspA) is an integral surface protein expressed during the tick cycle, and a validated vaccine target. There are at least 20 recognized Borrelia genospecies, that vary in OspA serotype. Traditional serotyping of Borrelia isolates using OspA-specific monoclonal antibodies is technically challenging and reagent-constrained. This study presents a new in silico sequence-based method for OspA typing using next-generation sequence data. Using a compiled database of over 400 Borrelia genomes encompassing all major genospecies, we characterized OspA diversity in a manner that can accommodate existing and new OspA types and then defined boundaries for classification and assignment of OspA types based on the sequence similarity. To accommodate potential novel OspA types, we have developed a new nomenclature: OspA in silico type (IST). Beyond the ISTs which corresponded to existing OspA serotypes (ST1-8), we identified nine additional ISTs which cover new OspA variants in B. bavariensis (IST9-10), B. garinii (IST11-12), and other Borrelia genospecies (IST13-17). Compared to traditional OspA serotyping methods, this new computational pipeline provides a more comprehensive and broadly applicable approach for characterization of OspA type and Borrelia genospecies to support vaccine development. Impact StatementAs the incidence of LD continues to rise, so does the need to maintain genomic surveillance of disease-causing Borrelia spp. and support clinical development of new vaccines. Towards this goal, introducing the OspA in silico type (IST) nomenclature scheme, as well as the open-source release of this OspA analysis pipeline, will enable characterization of novel Borrelia OspA types using NGS data without the need for traditional, antibody-based serotyping systems.

genomics↗

bioRxiv2023

Discovery of an APP-Selective BACE1 Inhibitor for Alzheimer's Disease

Inhibition of amyloid precursor protein (APP) beta-site cleaving enzyme 1 (BACE1; BACE) has been a target for Alzheimers disease (AD) therapeutic development, but has been impaired by off-target effects of clinically evaluated inhibitors, including inhibition of cleavage of non-APP substrates. Here, we report our identification of a BACE inhibitors series that are not only selective for the APP substrate, but also for BACE1 as the targeted enzyme. These APP-selective fluoro aminohydantoin (FAH) inhibitor compounds were identified by screening a compound library for inhibition of BACE cleavage of a maltose binding protein (MBP)-conjugated-APPC125 substrate followed by IC50 determination using the P5-P5 substrate assay. In multiple substrate and enzyme cell-free assays, the lead compound FAH65 displayed substrate selectivity for inhibition of APP cleavage, with little activity against BACE substrates neuregulin 1 (NRG1) or p-selectin glycoprotein ligand -1 (PSGL1). We also demonstrate FAH65 shows little inhibitory activity against the enzyme cathepsin D (Cat D) or BACE2. FAH65 inhibits production of BACE cleavage products soluble APP{beta} (sAPP{beta}) and the {beta} C-terminal fragment ({beta}CTF), as well as amyloid-{beta} (A{beta})1-40 and 1-42, in vitro in cells and in vivo in an animal model of AD. In a murine model of AD, FAH65 improved the discrimination score in the Novel Object Recognition (NOR) memory testing paradigm. The active enantiomer of FAH65, FAH65E(-), was obtained and tested in in vivo pharmacokinetic and pharmacodynamic (PK/PD) analysis, wherein it displayed good brain-penetrance and target engagement. Given its demonstrated selectivity for both enzyme and substrate, along with evidence it can improve cognitive performance in an animal model, FAH65 and its E(-) enantiomer merit continued pre-clinical development towards clinical testing as an APP-selective BACE1 inhibitor. Such a candidate would reduce A{beta} levels and overcome the deleterious effects of the non-selective BACE1 inhibitors that have failed in the clinic and potentially could be used as a maintenance therapy along with or following clearance of A{beta} from the brain with the approved antibody therapy for AD.

neuroscience↗

bioRxiv2022

PfaSTer: A ML-powered serotype caller for Streptococcus pneumoniae genomes

Streptococcus pneumoniae (pneumococcus) is a leading cause of morbidity and mortality worldwide. Although multi-valent pneumococcal vaccines have curbed the incidence of disease, their introduction has resulted in shifted serotype distributions that must be monitored. Whole genome sequence (WGS) data provides a powerful surveillance tool for tracking isolate serotypes, which can be determined from nucleotide sequence of the capsular polysaccharide biosynthetic operon (cps). Although software exists to predict serotypes from WGS data, their use is constrained by the requirement of high-coverage Next Generation Sequencing (NGS) reads. This can present a challenge in so far as accessibility and data sharing. Here we present PfaSTer, a method to identify 65 prevalent serotypes from individual S. pneumoniae genome sequences rather than primary NGS data. PfaSTer combines dimensionality reduction from k-mer analysis with machine learning, allowing for rapid serotype prediction without the need for coverage-based assessments. We then demonstrate the robustness of this method, returning >97% concordance when compared to biochemical results and other in-silico serotypers. PfaSTer is open source and available at: https://github.com/pfizer-opensource/pfaster.

bioinformatics↗

bioRxiv2022

Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

SARS-CoV-2 continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from [~]4,892,000 high-quality SARS-CoV-2 genomes in GISAID. Any mutations identified from comparison to the reference sequence (Wuhan-hu-1) were cataloged and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (alpha-, beta-, and gamma-coronaviruses). Additionally, we showed that over time the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the EUA approval of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals. ImportanceThe recent authorization of oral SARS-CoV-2 antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. Emergence of new variants, as well as selective pressure imposed by antiviral drugs themselves, raise concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.

genomics↗

bioRxiv2021

The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis

CTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. Whereas Ctcf+/+Boris+/+, Ctcf+/- Boris+/+, and Ctcf+/+Boris-/- males are fertile, Ctcf+/-Boris-/- (Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are "toxic" to fertility. Thus, a combined action of CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.

genomics↗

bioRxiv2021

Effects of forced cohesin eviction and retention on X-inactivation and autosomes

Depletion of architectural factors globally alters chromatin structure, but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Interestingly, cohesin loss disrupts Xi superstructure, unveiling superloops between escapee genes, with minimal effect on gene repression. By contrast, forced cohesin retention markedly affects Xi superstructure and compromises spreading of Xist RNA-Polycomb complexes, attenuating Xi silencing. Effects are greatest at distal chromosomal ends, where looping contacts with the Xist locus are weakened. Surprisingly, cohesin loss created an "Xi superloop" and cohesin retention created "Xi megadomains" on the active X. Across the genome, a proper cohesin balance protects against aberrant inter-chromosomal interactions and tempers Polycomb-mediated repression. We conclude that a balance of cohesin eviction and retention regulates X-inactivation and inter-chromosomal interactions across the genome.

molecular biology↗

bioRxiv2019

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

RNA has been classically known to play central roles in biology, including maintaining telomeres1, protein synthesis2, and in sex chromosome compensation in certain species3,4. At the center of these important biological systems are noncoding RNAs. While thousands of long noncoding RNAs (lncRNAs) have been identified in mammalian genomes5-8, attributing RNA-based roles to lncRNA loci requires an assessment of whether the observed effect could be due to DNA regulatory elements, the act of transcription, or the lncRNA transcript. Here, we use the syntenically conserved lncRNA locus, Functional intergenic repeating RNA element (Firre), that is located on the X chromosome as a model to discriminate between DNA- and RNA-mediated effects in vivo. To this end, we generated genetically defined loss-of-function, gain-of-function, and rescue mouse models for Firre and provide genetic evidence that the Firre locus produces a trans-acting RNA. We report that: (i) Firre mutant mice have cell-specific defects during hematopoiesis and changes in gene expression that can be rescued by induction of Firre RNA from a transgene in the Firre knockout background, (ii) mice overexpressing Firre from a transgene exhibit increased levels of pro-inflammatory cytokines and impaired survival upon exposure to lipopolysaccharide, and (iii) deletion of the Firre locus did not result in changes in local gene expression on the X chromosome in 9 different biological contexts, suggesting that Firre does not function by cis-acting RNA or DNA elements. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis and immune function.

immunology↗

bioRxiv2019

Aging-related hypometabolism in the anterior cingulate cortex mediates the relationship between age vs. executive function but not vs. memory in cognitively intact elders

Elucidating the pathophysiology of cognitive decline during aging in those without overt neurodegeneration is a prerequisite to improved diagnosis, prevention, and treatment of cognitive aging. We showed previously the anterior cingulate cortex (ACC) and adjacent medial prefrontal cortex (mPFC) are centers for aging-related metabolic dysfunction that correlate with age-associated cognitive decline in healthy volunteers. Here, we examine using the extensive and well-characterized ADNI dataset the hypothesis that ACC metabolism in healthy seniors functions as a mediator in the relationship between age and executive function. In agreement with our previous findings, highly significant correlations arose between age and metabolism; metabolism and fluency; and age and fluency. These observations motivated a mediation model in which ACC metabolism mediates the relationship between age and fluency score. Significance of the indirect effect was examined by Sobel testing and bootstrapping. In these cognitively intact seniors with \"typical aging,\" there was neither a correlation between age and memory scores nor between ACC metabolism and memory scores. The metabolism in a control region, the primary motor cortex, showed no correlation with age or ACC metabolism. These findings motivate further research into aging-related ACC dysfunction to prevent, diagnose, and treat the decline in executive function associated with aging in the absence of known neurodegenerative diseases.\n\nSIGNIFICANCE STATEMENTThe pathophysiology of aging-related cognitive decline remains unclear but the anterior cingulate cortex (ACC), a major component of the anterior human attention system, shows decreasing metabolism that correlates with declining executive function despite otherwise intact cognition. Here, the relationships between ACC metabolism, age, executive function, and memory were examined using the large, public, ADNI database. Earlier findings were confirmed. In addition, ACC metabolism was found a mediator between age and executive function. In contrast, no correlation arose between memory and age or between memory and ACC metabolism. No correlations surfaced when using the metabolism of the right primary motor cortex as a control region. Development of preventive medicine and novel treatments will require elucidation of aging-related ACC pathophysiology requiring further research.

neuroscience↗

bioRxiv2019

A preliminary study of brain metabolism in treatment-resistant depression before and after treatment with olanzapine-fluoxetine combination

Treatment-resistant depression (TRD) occurs in many patients and causes high morbidity and mortality. Because TRD subjects are particularly difficult to study especially longitudinally, biological data remain very limited. In a preliminary study to judge feasibility and power, 25 TRD patients were referred from specialty psychiatric practices. All were severely and chronically depressed and mostly had comorbid psychiatric disorders as is typical in TRD. Nine patients were able to complete all required components of the protocol that included diagnostic interview; rating scales; clinical magnetic resonance imaging; medication washout; treatment with maximally tolerated olanzapine-fluoxetine combination for 8 weeks; and pre- and post-treatment fluorodeoxyglucose positron emission tomography. This drug combination is an accepted standard of treatment for TRD. Dropouts arose from worsening depression, insomnia, and anxiety. One patient remitted; three responded. A priori regions of interest included the amygdala and subgenual cingulate cortex (sgACC; BA25). Responders showed decreased metabolism with treatment in the right amygdala that correlated with clinical response; no significant changes in BA25; better response to treatment the higher the baseline BA25 metabolism; and decreased right ventromedial prefrontal metabolism (VMPFC; broader than BA25) with treatment which did not correlate with depression scores. The baseline metabolism of all individuals showed heterogeneous patterns when compared to a normative metabolic database. Although preliminary given the sample size, this study highlights several issues important for future work: marked dropout rate in this study design; need for large sample size for adequate power; baseline metabolic heterogeneity of TRD requiring careful subject characterization for future studies of interventions; relationship of amygdala activity decreases with response; and the relationship between baseline sgACC and VMPFC activity with response. Successful treatment of TRD with olanzapine-fluoxetine combination shows changes in cerebral metabolism similar to those seen in treatment-responsive major depression.

neuroscience↗

bioRxiv2018

Unraveling the layers of cryptic genetic variation in a yeast gene regulatory network

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross. Mapping of the traits genetic basis after induction by three different genetic perturbations identifies 21 total loci. The perturbations largely uncover distinct loci, and strongly influence additivity, epistasis, and genotype-environment interaction among these loci. Only a single locus-- the coding region of the cell surface gene FLO11--is common to all three perturbations. While the remaining loci mostly influence FLO11 transcription in cis or trans, we detect loci in different pathways and sub-pathways in the presence of each perturbation. Our work shows that complex gene regulatory networks can harbor multiple layers of cryptic variation, each of which may only be visible in highly specific genotypic and environmental contexts.\n\nArticle SummaryThe extent and regulation of cryptic genetic variation within populations is not fully understood. To address these questions, we comprehensively dissect the genetic basis of a budding yeast colony trait following its induction by three different genetic perturbations. In total, we identify 21 distinct loci, most of which show phenotypic effects that depend on particular perturbations, other segregating loci, and temperature. We find that nearly all involved loci participate in a common gene regulatory network (GRN). Thus, our work demonstrates the large amount of cryptic variation underlying a single trait and ties the visibility of this variation to GRN activity.

genetics↗

bioRxiv2018

Megadomains and superloops form dynamically but are dispensable for X chromosome inactivation and gene escape

The mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for how the 3D genome is organized. The Xi shows weakened topologically associated domains and is instead organized into megadomains and superloops directed by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape silencing. Here, we find that megadomains do not precede Xist expression or Xi gene silencing. Deleting Dxz4 disrupts megadomain formation, whereas deleting Firre weakens intra-megadomain interactions. Surprisingly, however, deleting Dxz4 and Firre has no impact on Xi silencing and gene escape. Nor does it affect Xi nuclear localization, stability, or H3K27 methylation. Additionally, ectopic integration of Dxz4 and Xist is not sufficient to form megadomains on autosomes, further uncoupling megadomain formation from chromosomal silencing. We conclude that Dxz4 and megadomains are dispensable for Xi silencing and escape from X-inactivation.

genomics↗

bioRxiv2017

The Genomic Landscape Of Tree Rot In Phellinus noxius And Its Hymenochaetales Members

The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomics analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens, and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P. noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P. noxius has a bipolar heterothallic mating system, with unusual highly expanded ~60 kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P. noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single-nucleotide-polymorphisms (SNPs) with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.

genomics↗