Li-Jun Ma

Li-Jun Ma
University of Massachusetts Amherst | UMass Amherst · Department of Biochemistry and Molecular Biology

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264
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Publications

Publications (264)
Article
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Fungal effector proteins function at the interfaces of diverse interactions between fungi and their plant and animal hosts, facilitating interactions that are pathogenic or mutualistic. Recent advancements in protein structure prediction have significantly accelerated the identification and functional predictions of these rapidly evolving effector...
Article
Full-text available
Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most damaging plant diseases known. Foc race 1 (R1) decimated the Gros Michel-based banana (Musa acuminata) trade, and now Foc tropical race 4 (TR4) threatens global production of its replacement, the Cavendish banana. Here population genomics revealed that al...
Preprint
Full-text available
Fusarium oxysporum is a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations of F. oxysporum to animal or plant hosts, we conducted a comparative phenotypic and genetic...
Article
Full-text available
Course‐based Undergraduate Research Experiences (CUREs) integrate active, discovery‐based learning into undergraduate curricula, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the in...
Preprint
Full-text available
Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense ( Foc ), is one of the most damaging plant diseases recorded. Foc race 1 (R1) decimated the Gros Michel–based banana trade. Currently, tropical race 4 (TR4) is threatening the global production of its replacement cultivar, Cavendish banana. Population genomics and phylogenetics re...
Article
Full-text available
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects gl...
Preprint
Full-text available
Course-based Undergraduate Research Experiences (CUREs) integrate active, discovery-based learning into undergraduate curriculums, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the...
Preprint
Full-text available
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected g...
Article
Full-text available
The filamentous fungus Fusarium graminearum is a well-known cereal pathogen and F. avenaceum is a pathogen with a wide host range. Recently, both species were reported as causal agents of apple rot, raising concerns about postharvest yield losses and mycotoxin contamination. Here, we report genome assemblies of F. avenaceum KA13 and F. graminearum...
Chapter
Full-text available
The genome of Fusarium oxysporum, an ascomycete fungus, can be divided into two compartments: core chromosomes (CCs) and accessory chromosomes (ACs). CCs are conserved, vertically transmitted from parent to offspring, and involved in essential housekeeping functions, whereas lineage- or strain-specific ACs are horizontally transmitted and associate...
Article
Full-text available
Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains...
Preprint
Full-text available
Sweet basil ( Ocimum basilicum L.) production is threatened by the oomycete pathogen Peronospora belbahrii causing basil downy mildew (BDM); BDM resistant cultivar ‘Mrihani’ (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM- susceptible ‘Newton’ (SB22), but the molecular mechanisms con...
Article
Full-text available
MicroRNAs (miRNAs) are small non-coding RNAs that regulate protein-coding gene expression primarily found in plants and animals. Fungi produce microRNA-like RNAs (milRNAs) that are structurally similar to miRNAs and functionally important in various biological processes. The fungus Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of Bana...
Chapter
Fusarium oxysporum is a cross-kingdom fungal pathogen that not only causes devastating plant vascular diseases but can also opportunistically infect humans. Here we describe two high-throughput screening assays, a resazurin cell viability assay and an optical density assay, to screen natural products from cultured plant cells with antifungal proper...
Article
Full-text available
Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains shar...
Preprint
Full-text available
Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strain...
Article
Full-text available
Transposable elements (TEs) are mobile elements capable of introducing genetic changes rapidly. Their importance has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs has resulted in a growing number of bioinf...
Preprint
Transposable elements (TEs) are mobile genetic elements capable of rapidly altering the genome through their movements. The importance of TE activity has been documented in many biological processes, such as introducing genetic instability, altering patterns of gene expression, and accelerating genome evolution. Increasing appreciation of TEs resul...
Article
Full-text available
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agr...
Article
Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acqu...
Article
Full-text available
Here, we report a chromosome-level genome assembly of Fusarium oxysporum strain Fo47 (12 pseudomolecules; contig N50: 4.52Mb), generated using a combination of PacBio long-read, Illumina paired end and Hi-C sequencing data. Although F. oxysporum causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and widely...
Preprint
Here, we report a chromosome-level genome assembly of Fusarium oxysporum strain Fo47 (12 pseudomolecules; contig N50: 4.52Mb), generated using a combination of PacBio long-read, Illumina pair-ended and Hi-C sequencing data. Although F. oxysporum causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and widely...
Article
Full-text available
Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. He...
Article
Full-text available
Fusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in de...
Article
Motif identification has been one of the most widely studied problems in bioinformatics. Many methods have been developed to discover binding motifs from a large set of genes. But when the given genes are only a partial set of target genes, the statistical significance usually contains a bias towards the input. If we can identify the TF binding mot...
Article
Full-text available
Fusarium oxysporum is a pathogenic fungus that infects hundreds of plant species. This paper reports the improved genome assembly of a reference strain, F. oxysporum f. sp. lycopersici Fol4287, a tomato pathogen.
Chapter
Full-text available
Plant diseases cause significant losses to agricultural production and pose serious threats to food security worldwide. Understanding the mechanism of host–pathogen interaction is essential for the development of novel diagnostic methods and disease management strategies. RNA sequencing (or RNA-Seq) technology enables a global characterization and...
Article
Full-text available
Isolates of Fusarium oxysporum are adapted to survive a wide range of host and nonhost conditions. In addition, F. oxysporum was recently recognized as the top emerging opportunistic fungal pathogen infecting immunocompromised humans. The sensory and response networks of these fungi undoubtedly play a fundamental role in establishing the adaptabili...
Preprint
Full-text available
The Fusarium oxysporum species complex (FOSC) is a group of soil-borne pathogens causing severe disease in over one hundred plant hosts, while individual strains exhibit strong host specificity. Both chromosome transfer and comparative genomics experiments have demonstrated that lineage-specific (LS) chromosomes contribute to the host specific path...
Article
Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathog...
Article
Seventy-four F. oxysporum soil isolates were assayed for known effector genes present in an F. oxysporum f.sp. lycopersici race 3 tomato wilt strain (FOL MN-25) obtained from the same fields in Manatee County, Florida. Based on the presence or absence of these genes, four haplotypes were defined, two of which represented 96% of the surveyed isolate...
Conference Paper
The production of sweet basil (Ocimum basilicum) is threatened by the Oomycete downy mildew pathogen Peronospora belbahrii. However, economically viable cultivars lack usable resistance traits while some economically inviable cultivars display resistance. Through a comprehensive genetic breeding program, a resistant cultivar MRI showing resistance...
Chapter
Full-text available
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to...
Article
Full-text available
Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have develop...
Data
A complete protocol for performing metatranscriptomic data analysis using the pipeline.
Article
Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was...
Data
Table S6 Gene lists of eight regulatory modules (A–H) and complete FunCat analysis results
Data
Table S2 Input gene expression data matrix Table S5 List of 75 inferred transcription factor regulators and the most enriched binding sites for target genes Table S8 Shared networks by the Fusarium graminearum gene regulatory network (GRN) and protein–protein interaction network (FPPI)
Data
Fig. S1 Scatterplot matrix of three biological replicates and associated Pearson correlation coefficients (r) for each condition/biological state transcriptomically profiled in this study using the Affymetrix Fungal Multigenome ExonChip. Fig. S2 Bayesian network score distribution for the top 300 regulators in the Fusarium graminearum gene regulat...
Data
Table S3 Spreadsheets containing lists of candidate regulators, inferred 120 top regulators, the full gene regulatory network (GRN), core genome GRN and Fusarium graminearum‐specific GRN
Data
Table S7 Gene regulatory networks for candidate effector genes
Article
Full-text available
Head blight caused by Fusarium graminearum threatens world‐wide wheat production, resulting in both yield loss and mycotoxin contamination. We reconstructed the global F. graminearum gene regulatory network (GRN) from a large collection of transcriptomic data using Bayesian network inference, a machine‐learning algorithm. This GRN reveals connectiv...
Article
Full-text available
Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pis...
Data
Fig. S4 The aurofusarin biosynthesis gene cluster is up‐regulated in the Fusarium graminearum Δfac1 (mac1) mutant compared with the wild‐type (WT).
Data
Fig. S5 Comparison of differentially expressed genes (DEGs) in Fusarium graminearum (Fg) and F. verticillioides (Fv) Δfac1 and Δcpk1 mutants. The Venn diagram shows the number of DEGs in Fg and Fv Δfac1 mutants and the number of shared DEGs. Green and red represent down‐regulated and up‐regulated genes, respectively. The heat map displays the fold...
Data
Table S4 List of shared and distinct differentially expressed genes (DEGs) of Fusarium graminearum and F. verticillioides.
Data
Fig. S1 Quality control of the fungal multigenome ExonChip demonstrated in heatmaps of each fungal genomics DNA hybridization with the ExonChip. Genes are represented in columns and fungal samples in rows (from top to bottom: Puccinia graminis, Magnaporthe oryzae, three Fusarium oxysporum strains Fol 4287, MN25 and Fo47, F. graminearum, F. solani,...
Data
Fig. S2 Scatter plot matrix of gene expression levels in all hybridization samples of Fusarium graminearum used in this study. Entire gene expression values for all three replicates of all genetic backgrounds, i.e. wild‐type (WT) (FgCM), Δfac1 (FgFAC1) and Δcpk1 (FgCPK1), were plotted in a scatter plot matrix.
Data
Table S3 Summary of differentially expressed genes (DEGs) in Fusarium verticillioides Δfac1 and Δcpk1 mutants.
Data
Table S1 Array description: the array includes nine plant‐pathogenic fungal genomes and tiling probes for the whole genomes of Fusarium graminearum and F. oxysporum and partial genome of F. verticillioides.
Data
Table S2 Summary of differentially expressed genes (DEGs) in Fusarium graminearum Δfac1 and Δcpk1 mutants.
Data
Fig. S3 Scatter plot matrix of gene expression levels in all hybridization samples of Fusarium verticillioides used in this study, including the wild‐type (CM), Δfac1 (mac1) and Δcpk1 (cpka). Entire gene expression values for all three replicates of all genetic backgrounds, i.e. WT (Fv_CM), Δfac1 (Fv_mac1) and Δcpk1 (Fv_cpka), were plotted in a sca...
Data
Table S5 Gene expression levels and ratio of expression levels (ROELs) of orthologous genes in Fusarium graminearum and F. verticillioides.
Article
Full-text available
Magnaporthaceae is a family of ascomycetes that includes three fungi of great economic importance: Magnaporthe oryzae, Gaeumannomyces graminis var. tritici, and Magnaporthe poae. These three fungi cause widespread disease and loss in cereal and grass crops including rice blast disease (M. oryzae), take-all disease in wheat and other grasses (G. gra...
Article
Banana (Musa spp.) is one of the world's most valuable primary agricultural commodities. Exported fruit are key commodities in several producing countries yet make up less than 15% of the total annual output of 145 million metric tons (MMT). Transnational exporters market fruit of the Cavendish cultivars, which are usually produced in large plantat...
Article
Full-text available
The cyclic AMP (cAMP)-PKA pathway is a central signaling cascade that transmits extracellular stimuli and governs cell responses through the second messenger cAMP. The importance of cAMP signaling in fungal biology has been well documented and the key conserved components, adenylate cyclase (AC) and the catalytic subunit of PKA (CPKA), have been fu...
Article
Full-text available
Basil (Ocimum spp.) is one of the most economically-important and widely-grown herbs in the world. Basil downy mildew, caused by Peronospora balbahrii, has become an important disease in word-wide sweet basil (O. basilicum) production in the past decade leading to devastating crop losses. Global sweet basil production is at significant risk to basi...
Article
Full-text available
Chaetomium globosum is a filamentous fungus typically isolated from cellulosic substrates. This species also causes superficial infections of humans and, more rarely, can cause cerebral infections. Here, we report the genome sequence of C. globosum isolate CBS 148.51, which will facilitate the study and comparative analysis of this fungus.
Conference Paper
Genus Fusarium contains pathogens that infect hundreds of crop plants as well as humans and thus threatens global food safety and human health. Diseases caused by this group of organisms are modulated by their Gene Regulatory Networks (GRNs). Reconstructing GRNs that dynamically control all cellular functions will enable a comprehension of the comp...
Article
Full-text available
Horizontal chromosome transfer introduces host-specific pathogenicity among members of the Fusarium oxysporum species complex and is responsible for some of the most destructive and intractable plant diseases. This paper reports the genome sequence of F. oxysporum f. sp. melonis (NRRL 26406), a causal agent of Fusarium wilt disease on melon. FOOTNO...
Chapter
Full-text available
The filamentous ascomycete Fusarium graminearum has been studied intensively over decades. The fungus causes disease and produces mycotoxins on cereal crops, such as wheat, barley, and maize, threatening global food safety and human health. There is no effective approach to manage the disease or control mycotoxin production due to our limited under...
Article
Full-text available
Ustilaginoidea virens (Cooke) Takah is an ascomycetous fungus that causes rice false smut, a devastating emerging disease worldwide. Here we report a 39.4 Mb draft genome sequence of U. virens that encodes 8,426 predicted genes. The genome has ~25% repetitive sequences that have been affected by repeat-induced point mutations. Evolutionarily, U. vi...
Conference Paper
Full-text available
In recent years, constructing regulatory networks using gene expression data has received extensive attentions. From Boolean network, Bayesian network to Module network, a number of models have been applied in order to learn the regulatory networks more accurately. The statistical power of network modeling is directly affected by sample size of ava...
Chapter
Introduction Determinants of Pathogenicity within the Genus Fusarium Evolution of Pathogenicity Revealed through Fusarium Comparative Genomics Evolution of Secondary Metabolite Gene Clusters Associated with Pathogenicity Conclusion
Article
Full-text available
Fusarium is a genus of filamentous fungi that contains many agronomically important plant pathogens, mycotoxin producers, and opportunistic human pathogens. Comparative analyses have revealed that the Fusarium genome is compartmentalized into regions responsible for primary metabolism and reproduction (core genome), and pathogen virulence, host spe...