Biology subjects

Hong, K.

Publications and source records attributed to Hong, K..

18 recordsLinked to original sources

bioRxiv2026

Virtual experiments bridge sequence and microscopy with generative models

Large-scale screening and mapping efforts have produced vast libraries of perturbation-readout data. Converting these measurements into mechanistic insights requires models that link perturbation and genetic input to phenotypes, i.e., labels from experimental readouts, which are usually task specific. We propose a different, virtual experiment modeling approach: train generative models to recreate readouts conditioned on the experimental context, and then let established downstream models extract phenotypes from the synthetic data. As an illustrative case, we develop a bidirectional sequence-image generative framework, CELL-FM, that maps protein sequence and cellular context to fluorescence microscopy images and back, enabling in silico localization prediction, image-conditioned functional motif analysis and generation, and large-scale virtual mutagenesis revealing the amino acid features controlling condensate formation of intrinsically disordered peptides. This approach decouples representation learning from task-specific annotation, reuses rich experimental modalities across many downstream tasks, and preserves the spatial and organizational detail that hand-crafted labels often discard.

bioinformatics↗

bioRxiv2026

Smallpox Vaccine Elicits CD8+ T Cell Immunity Persisting Over Four Decades with Cross-Recognition of Monkeypox Virus

Monkeypox, caused by MPXV, has become a global public health concern; however, the T-cell immunity against MPXV following smallpox vaccination remains unclear. In this study, we screened the immunogenicity of 21 predicted MPXV epitopes and compared immune responses between young and elderly groups. Two immunogenic CD8 T-cell epitopes, M15 and M17, were identified, both of which effectively stimulated specific immune responses, with significantly stronger responses observed in the young group. Notably, this study provides the first evidence that smallpox vaccination induces CD8 T-cell immunity that cross-recognizes the MPXV epitopes M15 and M17 and remains detectable for more than four decades after vaccination, as demonstrated in vaccinated individuals aged 53-75. These findings provide experimental evidence for understanding the cross-protective mechanisms of the smallpox vaccine and informing monkeypox vaccine development.

immunology↗

bioRxiv2026

Cryo-EM structures of Arabidopsis PRC2 histone methyltransferase isoforms reveal a differential regulatory mechanism

Polycomb Repressive Complex 2 (PRC2) is a histone H3K27 methyltransferase that represses gene expression. Arabidopsis thaliana (A. thaliana) has several different PRC2 isoforms that are functionally distinct during the life cycle of the plants. However, their biochemical and structural characteristics have not been investigated. Here, we biochemically characterized PRC2 isoforms having different catalytic subunits: SWNINGER (SWN; PRC2SWN) and CURLY LEAF (CLF; PRC2CLF). Interestingly, PRC2SWN showed much lower activity than PRC2CLF. In addition, PRC2SWN methylates histone H3K27 in mono and di-methylation, while PRC2CLF shows robust tri-methylase activity. We also determined the cryo-electron microscopy (cryo-EM) structures of PRC2SWN and PRC2CLF, revealing that the substrate binding pocket of the SWN SET domain is blocked by a loop in the pre-SET domain, functioning as an auto-inhibitory loop, while that of the CLF SET domain is freely accessible. Introduction of CLF-like mutations in the auto-inhibitory loop in SWN enhances PRC2SWN activity. Furthermore, structure-guided in planta analysis shows that a CLF-mimetic SWN mutant rescues the CLF knockout phenotype. Our work provides structural and molecular insights into the isoform-specific regulatory mechanism of plant PRC2.

Plant Biology↗

bioRxiv2026

Microenvironmental Determinants of Reaction Kinetics in Biomolecular Condensates Probed with Protein Ligation

Cells utilize liquid-liquid phase separation to organize biochemical reactions within biomolecular condensates, which function as membraneless organelles. Although these assemblies are known to enhance reaction rates by concentrating reactants, the mechanisms beyond simple mass-action effects remain poorly understood. Here, we examined how the physicochemical microenvironment within condensates modulates reaction kinetics using spontaneous protein ligation as a model reaction, conducting a systematic analysis across various condensates, ranging from structured scaffolds (PRM-SH3 systems) to intrinsically disordered protein (IDP)-based scaffolds such as LAF, TAF, and FUS. We designed a FRET-based proximity-sensitive client probe to quantify increases in effective local concentration arising from excluded-volume effects. In parallel, we measured internal hydrophilicity and water activity, revealing them as additional key determinants of reaction acceleration. Together, the findings presented here elucidate how phase-separated compartments regulate biochemical reactions through the interplay of physical (effective concentration) and chemical (hydrophilicity and water activity) microenvironments and provide mechanistic insights for engineering condensates with tunable reactivity.

biochemistry↗

bioRxiv2025

Biosynthesis of a major plant immunity hormone, salicylate, changed drastically during evolution of flowering plants

Salicylate (SA) is a major plant immunity hormone that activates immune responses against biotrophic pathogens. Between two known SA biosynthetic routes, the isochorismate synthase (ICS) and phenylalanine ammonia-lyase (PAL) pathways, which predominates in particular flowering plants has remained uncertain. We established a straightforward approach that directly quantifies the relative contributions of the ICS and PAL pathways and can also reveal an alternative, non-ICS/PAL route. In this approach, SA and shikimate (ShA), the precursor of SA in the ICS and PAL pathways, were metabolically labeled with [13C6]glucose in leaf tissue. We analyzed the LC-MS/MS data of the compounds using a metabolism-guided statistical model (the ICS-PAL model). This analysis allowed tracking of the origins of their ring and carboxyl carbons and, consequently, determination of the main SA biosynthetic routes. We surveyed SA biosynthetic routes in plants of the order Brassicales, other diverse eudicots, a monocot, magnoliids, and basal angiosperms. We found that the main SA biosynthetic routes changed at least twice during evolution of flowering plants: from a non-ICS/PAL pathway to the PAL pathway around the divergence time of monocots, and from the PAL pathway to the ICS pathway within Brassicales. Application of another metabolism-guided statistical model (the PKS-PAL model) to the SA data suggested that the non-ICS/PAL pathway involves a type III polyketide synthase (PKS). Typically, once a biosynthetic pathway is established for an important molecule, it is conserved in the subsequent lineage. SA biosynthesis in flowering plants took an unusual evolutionary path in which the pathways changed drastically multiple times. This unconventional evolutionary mechanism was employed for a major immunity hormone, likely due to rapid evolution of biotic environments, such as pathogens and insects that attack plants.

plant biology↗

bioRxiv2025

De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy

De novo protein design has emerged as a powerful strategy with the promise to create new tools. The practical performance of designed fluorophore binders, however, has remained far from meeting fluorescence microscopy demands. Here, we design de novo Rhodamine Binder (Rhobin) tags that combine ideal properties including size, brightness, and now adding hyperstability. Rhobin allows live and fixed cell imaging of a wide range of subcellular targets in mammalian cells. Its reversible fluorophore binding further enables live super-resolution STED microscopy with low photobleaching, as well as PAINT-type single-molecule localization microscopy. We showcase Rhobin in the extremophile Sulfolobus acidocaldarius living at 75{degrees}C, an application previously inaccessible by existing tags. Rhobin will serve as the basis for a new class of live cell fluorescent tags and biosensors.

bioengineering↗

bioRxiv2025

Evolutionary Trade-off Between Stomatal Defense and Gas Exchange in Brassicaceae

Stomatal opening is crucial for gas exchange, but it unavoidably offers invasion by pathogens. In response, plants close stomata to prevent pathogen entry, while the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) produces coronatine (COR), a jasmonate (JA) mimic, to counteract this plant response. Here, we demonstrate that by COR, Pto exploits CYP707A1 activation in Arabidopsis thaliana, encoding an enzyme that degrades abscisic acid, essential for stomatal closure. Notably, COR-induction of CYP707A1 is absent in other Brassicaceae species, such as Capsella rubella and Eutrema salsugineum, rendering them resistant to Pto invasion. In contrast, in A. thaliana, CYP707A1 enables rapid stomatal opening at dawn in a JA-dependent manner, enhancing gas exchange and chlorophyll content, unlike C. rubella and E. salsugineum. Promoter-swap experiments confirm that the regulatory region of CYP707A1 underlies these evolutionary diversifications. Together, our study presents a mechanism underlying an evolutionary trade-off between stomatal defense and gas exchange.

plant biology↗

bioRxiv2025

Emergence of isochorismate-based salicylic acid biosynthesis within Brassicales

Salicylic acid (SA) is a major defense phytohormone. In Arabidopsis thaliana, the isochorismate (IC) pathway is the primary route for pathogen-induced SA biosynthesis. First, the IC synthase (ICS) catalyzes the isomerization of chorismate to IC in chloroplasts. Second, the chloroplast-localized MATE transporter EDS5 appears to transport IC from chloroplasts to the cytosol. Cytosolic IC is then further converted to SA via the GH3 amino acid-conjugating enzyme PBS3. While this pathway is genetically well-characterized in A. thaliana, its evolutionary origin and conservation remain controversial. In this study, through comprehensive phylogenetic, structural, and functional analyses, we demonstrate that the IC pathway emerged within the Brassicales order in a time span between the divergence of Carica papaya and Capparis spinosa. The evolution of the IC pathway was driven by three key adaptations during the time span: (1) enhancement of ICS activity, (2) neofunctionalization of EDS5 after duplication of its ancestral gene, and (3) evolution of a PBS3, whose activity is specialized for glutamate-conjugation to IC. Structural modeling and functional assays reveal that an enhanced salt bridge network in ICS enhanced its activity. One of the duplicated genes, EDS5, acquired key amino acid substitutions in the C-lobe, which likely contributed to the EDS5 neofunctionalization. In addition, the functional PBS3 clade, including A. thaliana PBS3, is restricted to a Brassicales clade. Taken together, this study addresses the evolutionary trajectory of IC-based SA biosynthesis.

plant biology↗

bioRxiv2024

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

The crisis of biodiversity loss in the anthropogenic era requires new tools for studying non-model organisms. Elephants, for example, are both an endangered species and excellent models studying complex phenotypes like size, social behavior, and longevity, but they remain severely understudied. Here we report the first derivation of elephant (Elephas maximus) induced pluripotent stem cells (emiPSCs) achieved via a two-step process of chemical-media induction and colony selection, followed by overexpression of elephant transcription factors OCT4, SOX2, KLF4, MYC {+/-} NANOG and LIN28A, and modulation of the TP53 pathway. Since the seminal discovery of reprogramming by Shinya Yamanaka, iPSCs from many species including the functionally extinct northern white rhinocerous have been reported, but emiPSCs have remained elusive. While for multiple species the reprogramming protocol was adopted with little changes compared to model organisms like mouse and human, our emiPSC protocol requires a longer timeline and inhibition of TP53 expansion genes that are hypothesized to confer unique cancer resistance in elephants. iPSCs unlock tremendous potential to explore cell fate determination, cell and tissue development, cell therapies, drug screening, disease modeling, cancer development, gametogenesis and beyond to further our understanding of this iconic megafauna. This study opens new frontiers in advanced non-model organism cellular models for genetic rescue and conservation.

cell biology↗

bioRxiv2022

Comprehensive Structural Variant Detection: From Mosaic to Population-Level

Long-read Structural Variation (SV) calling remains a challenging but highly accurate way to identify complex genomic alterations. Here, we present Sniffles2, which is faster and more accurate than state-of-the-art SV caller across different coverages, sequencing technologies, and SV types. Furthermore, Sniffles2 solves the problem of family- to population-level SV calling to produce fully genotyped VCF files by introducing a gVCF file concept. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we successfully identified multiple mosaic SVs across a multiple system atrophy patient brain. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements. In summary, we demonstrate the utility and versatility of Sniffles2 to identify SVs from the mosaic to population levels.

bioinformatics↗

bioRxiv2021

Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

The northern white rhinoceros (NWR; Ceratotherium simum cottoni) is functionally extinct, with only two females remaining alive. Efforts to rescue the NWR have inspired the exploration of unconventional conservation methods, including the generation of artificial gametes from induced pluripotent stem cells and somatic cell nuclear transfer. To enable the technologies required for these approaches, we used complementary sequencing and mapping methods to generate a NWR chromosome-level reference genome that meets or exceeds the metrics proposed by the Vertebrate Genome Project. It represents 40 autosomes, an X and a partially-resolved Y chromosome, and the mitochondrial genome. We compared the NWR reference genome to the southern white rhinoceros (SWR) population that has been physically separated from the NWR for tens of thousands of years. Using short-read data from the SWR and optical mapping, we found that the two populations are very similar on both the chromosome level and mitochondrial genome level. The results of this study are encouraging for the efforts underway to rescue the NWR.

genomics↗

bioRxiv2021

A trimeric NTD and RBD SARS-CoV-2 subunit vaccine induced protective immunity in CAG-hACE2 transgenic mice and rhesus macaques

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to significant public health, economic and social problems. Development of effective vaccines is still a priority to contain the virus and end the global pandemic. In this study, we reported that ReCOV, a recombinant trimeric NTD and RBD two-component SARS-CoV-2 subunit vaccine adjuvanted with BFA03 (an AS03-like squalene adjuvant), induced high levels of neutralizing antibodies against SARS-CoV-2 and the circulating variants in mice, rabbits and rhesus macaques. Notably, two-dose immunizations of ReCOV provided complete protection against challenge with SARS-CoV-2 in hACE2 transgenic mice and rhesus macaques, without observable antibody-dependent enhancement of infection. These results support further clinical development of ReCOV and the vaccine is currently being evaluated in a phase I clinical trial in New Zealand (NCT04818801).

immunology↗

bioRxiv2021

Endothelial alpha globin is a nitrite reductase

Small artery vasodilation in response to hypoxia is essential for matching oxygen supply to tissue oxygen demand. One source of hypoxic dilation via nitric oxide (NO) signaling is nitrite reduction by erythrocytic hemoglobin (2{beta}2). However, the alpha subunit of hemoglobin is also expressed in resistance artery endothelium and localized to myoendothelial junctions, a subcellular domain that contacts underlying vascular smooth muscle cells. We hypothesized that nitrite reduction mediated by endothelial alpha globin may occur at myoendothelial junctions to regulate hypoxic vasodilation. To test this concept, we created two novel mouse strains: one lacking alpha globin specifically in endothelium (EC Hba1{Delta}/{Delta}) and one where alpha globin is mutated such that its inhibitory association with endothelial NO synthase (eNOS) is prevented (Hba1WT/{Delta}36-39). In EC Hba1{Delta}/{Delta} or Hba1WT/{Delta}36-39 mice hemoglobin levels, hematocrit and erythrocyte counts were unchanged from littermate controls. Loss of the full alpha globin protein from the endothelium in the EC Hba1{Delta}/{Delta} model was associated with decreased exercise capacity and decreased intracellular nitrite utilization in hypoxic conditions. These effects were not seen in Hba1WT/{Delta}36-39 animals. Hypoxia induced vasodilation was decreased by 60% in isolated thoracodorsal arteries from EC Hba1{Delta}/{Delta}, while infusion of erythrocytes only partially rescued the dilatory response. Lastly, unlike other models where blood pressure is decreased, EC Hba1{Delta}/{Delta} blood pressure was not altered in response to hypoxia. Overall, we conclude that alpha globin in the resistance artery endothelium can act as a nitrite reductase to provide a local vasodilatory response to hypoxia.

physiology↗

bioRxiv2020

Multiple Mechanisms of HIV-1 resistance to PGT135 in Chinese Subtype B' Slow Progressor

In our study, we describe a slow progressor CBJC515 from whom we constructed pseudoviruses expressing autologous Env. We surprisingly found all the pseudoviruses were resistant to PGT135. By making site-directed mutations and chimeric Env constructs, we found the early 05 strains escaped from PGT135 by losing the N332 glycan site, while the later 06 and 08 strains may escape with the retention of key epitopes through the change of V1/V4/C2 region or by N398/N611 glycan, which was selected as unique N-glycosylation site of CBJC515 compared with CBJC437 whose viruses were also harboring key epitopes but sensitive to PGT135. These findings provide insights into how HIV-1 can escape from N332-directed broadly neutralizing antibody (bNAb) responses without changing the epitope itself, and these ways may be useful to prolong the exposures of bNAb epitopes and contribute to bNAb development. Furthermore, our chimeric experiments also allowed us to explore the co-evolution and retention of functionality among regions. We confirmed that the V1V2 region has a wide range of effectiveness in interfering with the function of envelope protein and the V3 region can promote protein function recovery and buffer the harmful polymorphisms in the other regions contributing to the Env antigenic diversity. These results may provide some clues for the design of vaccines against HIV-1 strains. IMPORTANCEOur findings of mechanisms escaping from PGT135 verified the extensive role of long V1 region in mediating escape from V3-bNAbs. In addition, we also found multiple additional ways suggested that extreme variation may be needed by HIV-1 to escape from PGT135 without changing the epitope itself. Although the V3-glycan bNAb responses are among the most promising vaccine targets, as they are commonly elicited during infection, our findings indicated there may be additional difficulties to be taken into account in immunogen design, such as the consideration of other regions and some glycosylation sites affecting the mask of key epitopes, as well as the selection pressure that may be required by other bNAbs. Our chimeric experiment also highlighted the key role of V3 region in contributing to the maintenance of Env diversity by buffering deleterious polymorphisms, which may be helpful for vaccine design.

immunology↗

bioRxiv2020

A Single Nucleotide Polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated North American Cannabis

BackgroundThe taxonomic classification of the Cannabis genus has been delineated through three main types: sativa (long and less branched plant with long and narrow leaves), indica (short but highly branched plant with broader leaves) and ruderalis (wild type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origin of each group and putative chemotypic and pharmacology. MethodsHere we describe a thorough investigation of cannabis accessions using a set of 22 highly informative and polymorphic SNP markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations and demonstrate the utility of this assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education. ResultsThe main outcomes are the identification of 5 clusters in the sample set available, including industrial hemp, resin hemp which likely underwent a bottleneck to stabilize CBDA accumulation (Type II & III). THC resin (type I) make up the other three clusters with terpinolene (colloquial "sativa" or "NLD"), myrcene/pinene and myrcene/limonene (colloquial "indica", "BLD"), which also putatively harbour an active CBCAS. ConclusionThe functional basis of key traits is also discussed as recently enabled by the NCBI Cannabis sativa Annotation Release 100, allowing for hypothesis testing with regards to secondary metabolite production as well as other key traits of importance for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.

plant biology↗

bioRxiv2019

Changes in the expression of mitochondrial morphology-related genes during the differentiation of murine embryonic stem cells

During embryonic development, cells undergo changes in gene expression, signaling pathway activation/inactivation, metabolism, and intracellular organelle structures, which are mediated by mitochondria. Mitochondria continuously switch their morphology between elongated tubular and fragmented globular via mitochondrial fusion and fission. Mitochondrial fusion is mediated by proteins encoded by Mfn1, Mfn2, and Opa1, whereas mitochondrial fission is mediated by proteins encoded by Fis1 and Dmn1L. Here, we investigated the expression patterns of mitochondria-related genes during the differentiation of mouse embryonic stem cells (ESCs) in response to leukemia inhibitory factor (LIF) withdrawal. The expression of Mfn2 and Dnm1L was, as expected, increased and decreased, respectively. By comparing gene expression and mitochondrial morphology, we proposed an index that could precisely represent mitochondrial changes during the differentiation of pluripotent stem cells by analyzing the expression ratios of three fusion- and two fission-related genes. Surprisingly, increased Mfn2/Dnm1L ratio was correlated with elongation of mitochondria during the differentiation of ESCs. Moreover, application of this index to other specialized cell types revealed that neural stems cells (NSCs) and mouse embryonic fibroblasts (MEFs) showed increased Mfn2/Dnm1L ratio compared to ESCs. Thus, we suggest that the Mfn2/Dnm1L ratio could reflect changes in mitochondrial morphology according to the extent of differentiation.

cell biology↗

bioRxiv2019

The signaling mechanism of Hcy-induced atrial fibrosis mediated by TRPC3

BackgroundHigh plasma levels of homocysteine (Hcy) are regarded as a risk factor for atrial fibrillation (AF), which is closely associated with the pathological consequence of atrial fibrosis and can lead to heart failure with a high mortality rate; Currently, there is no effective therapy for preventing atrial fibrosis, owing to a lack in fundamental understanding of the underlying mechanism. Here, we show that atrial fibrosis is mediated by the relationship between canonical transient receptor potential 3 (TRPC3) channels and sirtuin type 1 (SIRT1) under the stimulation of Hcy.\n\nMethodsThe left atrial appendage was obtained from patients with either sinus rhythm (SR) or AF, who underwent cardiothoracic surgery, and used to evaluate the relationship between the concentration of Hcy and a potential mechanism of cardiac fibrosis mediated by TRPC3 and SIRT1. We next performed transverse aortic constriction (TAC) in mouse to investigate the relationship. The mechanisms underlying atrial fibrosis involving TRPC3 and SIRT1 proteins were explored by co-immunoprecipitation (co-IP), bio-layer interferometry (BLI) and lentivirus transfection experiments. Quantitative polymerase chain reaction (qPCR) and western blotting (WB) were performed to analyse gene and protein expression, respectively.\n\nResultsThe majority of AF patients displayed atrial fibrosis, as demonstrated by Masson staining and immunohistochemistry. In the mouse model of TAC, more severe fibrosis was detected in the high-Hcy diet (HH) group, compared to NH mice; and the duration of induced AF was longer in the HH groups than in the normal diet (NH) group. Moreover, the HH group exhibited higher expression levels of TRPC3 and related fibrosis proteins, such as TGF-{beta} and Col-I, than the NH group, despite also showing a higher level of SIRT1 was observed. The activator of SIRT1 (Resveratrol, Res) attenuated the enhancement of TRPC3 and decrease in SIRT1 observed in the HH group. Further cell culture experiments confirmed that Hcy could promote the proliferation and differentiation of fibroblasts, the up-regulation of TRPC3, and the decrease in the protein level of SIRT1. Ultimately, the results of Co-IP and BLI indicated a direct interaction between TRPC3-C terminal domain (569-863) and SIRT1 proteins, in which the two proteins are antagonistic and in combination regulate the pathogenesis of atrial fibrosis.\n\nConclusionsThe higher level of atrial fibrosis were observed in the HH mouse group, compared with the NH mice group, Such results suggest that AF patients may be more susceptible to atrial fibrosis and possess a high probability of progressing to hyperhomocysteinemia. Moreover, our findings are consistent with the hypothesis that TRPC3 channel up-regulation leads to abnormal accumulation of collagen, with the down-regulation of SIRT1 as an aetiological factor of high Hcy, which in turn predisposes to atrial fibrosis and strongly enhances the possibility of AF.

molecular biology↗

bioRxiv2018

The Population Genetic Variation Analysis of Bitter Gourd Wilt Caused by Fusarium oxysporum f. sp. momordicae in China by Inter Simple Sequence Repeats (ISSR) Molecular Marker

The bitter gourd fusarium wilt caused by Fusarium oxysporum f.sp. momordicae (FOM) was a devastating disease in China and leading to great economic losses every year. A total of 152 isolates, which have the typical Fusarium oxysporum characteristics with abundant microconidia and macroconidia on the white or ruby colonies, were obtained from diseased plant tissues with typical fusarium wilt symptoms. The BLASTn analysis of rDNA-ITS showed 99% identity with F.oxysporum species. Among the tested isolates, three isolates infected tower gourd, and five isolates were pathogenic to bottle gourd. However, they were all pathogenic to bitter gourd. Based on the molecular and morphologic results, the isolates were identified as FOM. For genetic variation analysis, forty ISSR primers were screened and eleven primers were used in PCR amplification. Totally, 121 loci were detected, of which 52 loci were polymorphic at rate of 42.98%. The POPGENE analysis showed that Neis gene diversity index (H) and Shannons information index (I) were 0.0902 and 0.1478, respectively, which indicated that the genetic diversity for the tested 152 isolates was relatively low. It also means that each geographical population was a relatively independent unit. While the value of coefficient of gene differentiation (Gst=0.4929 > 0.15) pointed to the genetic differentiation was mainly among populations. The strength of gene flow (Nm=0.5143<1.0) was weaker, indicating that gene exchanges were blocked to some degree. The dendrogram based on ISSR markers showed that the eight geographical populations were clustered into four groups at the threshold of genetic similar coefficient 0.96. Fujian, Jiangxi and Guangdong populations were clustered into Group I. Group II contained Hunan and Guangxi populations. Group III only had Hainan population. Group IV consisted Shandong and Henan populations. The geographical populations closer to each other grouped together, suggesting a correlationship between geographical origin and genetic differentiation. Two hybridization events were observed between Hainan and Hunan populations and between Guangdong and Guangxi by Structure analysis. Our findings enrich the knowledge on genetic variation characteristics of the FOM populations with helpful of development of effective disease management programs and disease resistance breeding.

microbiology↗