Gap-free comparative genomics uncover virulence factors for Fusarium wilt of watermelons.

Watermelon (Citrullus lanatus L.) is a globally important fruit crop, yet it is susceptible to devastating diseases such as vascular wilt caused by Fusarium oxysporum f. sp.

Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen.

Genomes of clonally reproducing fungal pathogens are often compartmentalized into conserved core and lineage-specific accessory regions (ARs), enriched in transposable elements (TEs). ARs and TEs are thought to promote pathogen adaptation, but direct experimental evidence is sparse. Using an evolve and re-sequence approach, we found that serial passaging of the cross-kingdom fungal pathogen Fusarium oxysporum through tomato plants or axenic media rapidly increased fitness under the selection condition.

Host-specific adaptation in correlates with distinct accessory chromosome content in human and plant pathogenic strains.

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 to animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato []).

Super pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement.

Grapevine (Vitis) is one of the oldest domesticated fruit crops with great cultural and economic importance. Here we assembled and annotated haplotype-resolved genomes of 72 global Vitis accessions including 25 wild and 47 cultivated grapevines, among which genomes for 60 grapevines are newly released. Haplotype-aware phylogenomics disentangled the mysterious hybridization history of grapevines, revealing the enormous genetic diversity of the Vitis genus.

A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen.

Fusarium oxysporum is an asexual filamentous fungus that causes vascular wilt in hundreds of crop plants and poses a threat to public health through Fusariosis. F. oxysporum f.

Virulence of strains causing corneal or plant disease is associated with their distinct accessory chromosomes.

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 to animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato []).

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C.

FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.

Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans.

CUR(E)ating a new approach to study fungal effectors and enhance undergraduate education through authentic research.

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 instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges.

Conservation and Expansion of Transcriptional Factor Repertoire in the Species Complex.

The species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions.

CUR(E)ating a New Approach to Study Fungal Effectors and Enhance Undergraduate Education through Authentic Research.

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 instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges.

Conservation and Expansion of Transcriptional Factor Repertoire in the Species Complex.

The species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspected global transcription factor profiles (TFomes) and their potential roles in coordinating CCs and ACs functions to accomplish host-specific pathogenicity.

Genome Sequence Resource of TaB10 and KA13, Causal Agents of Stored Apple Rot.

The filamentous fungus is a well-known cereal pathogen and 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 KA13 and TaB10, both isolated from fruits with symptoms of apple rot.

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.

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 bioinformatics software to identify insertion events.

Genome Sequence of f. sp. , a Brassicaceae Pathogen.

The filamentous fungus is a soilborne pathogen of many cultivated species and an opportunistic pathogen of humans. f. sp.

Improved Assembly of Reference Genome Fusarium oxysporum f. sp. lycopersici Strain Fol4287.

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.

Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.

The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance.