Isheng Jason Tsai

High culturable diversity and climate-associated seasonal dynamics of Saccharomycotina yeasts in subtropical forest leaf litter

The paper samples and analyzes Saccharomycotina yeasts in subtropical forest leaf litter, revealing high culturable diversity and seasonal dynamics linked to climate factors.

A haploid wild yeast resource for exploring the natural ecology of Saccharomyces cerevisiae

This paper establishes a haploid yeast strain collection to study ecological and reproductive divergence in wild S. cerevisiae, finding that structural genomic variation and metabolic gene divergence drive these traits.

A global synthesis of yeast in microbiomes

This study synthesizes global yeast distribution in microbiomes using metabarcoding data, showing their ubiquity and underrepresentation despite ecological importance.

Dynamic evolution of AT-rich isochores shapes the genome of an intertidal fungus Annulohypoxylon annulatoides

The paper investigates the genomic adaptation of an intertidal fungus, identifying AT-rich isochores that may influence genome organization and stress response.

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid

The paper uses genomic and ecological data to show that a critically endangered salmonid population has hidden resilience and supports targeted conservation strategies.

Spatiotemporal dynamics and assembly process differ in fungal communities across contiguous habitats in tropical forests

The paper examines fungal community composition across contiguous habitats in tropical forests, finding that spatial scale and habitat influence assembly processes differently, with deterministic and stochastic factors shaping communities in leaves/twigs versus soil.

Living xylem cells encode a large number of conserved gene families responsible for vascular sap peptides

The paper identifies 4,804 sap peptide precursor genes in Populus trichocarpa, revealing their conservation across angiosperms and active expression in xylem during growth transitions.

A Sap Peptide Conserved across Flowering Plants Positively Regulates Lignin Biosynthesis, Biomass and Immunity

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

The paper uses MDA and ONT to sequence genomes and transcriptomes of nematodes, revealing genome diversity and phylogenetic relationships.

The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes

The paper analyzes six Aphelenchoides genomes to identify horizontal gene transfers in the last common ancestor of free-living and plant-parasitic nematodes, revealing major HGT events from bacteria, fungi, and plants.

Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen

This study identifies horizontal gene transfer events in Armillaria fungi that contribute to plant biomass degradation and pathogenicity.

Detecting intragenic trans-splicing events with hybrid transcriptome sequencing in cancer cells

This study develops NCLscan-hybrid to detect intragenic trans-spliced RNAs in cancer cells and validates their role in tumor growth and apoptosis.

Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories

This study samples S. cerevisiae genetic diversity in Taiwan, revealing nine lineages, historical admixture, and clonal reproduction, highlighting its natural diversity before human domestication.

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

This study sequenced FSSC genomes to reveal compartmentalisation patterns and pathogenic mechanisms in animal hosts.

Genomes of keystone Mortierella species lead to better in silico prediction of soil mycobiome functions from Taiwan's offshore islands

The paper uses genomic data from Mortierella species to improve in silico prediction of soil mycobiome functions across Taiwan's offshore islands.

Mycena genomes resolve the evolution of fungal bioluminescence

The paper sequenced genomes of five bioluminescent Mycena fungi to study the evolution of luciferase clusters and bioluminescence, finding that the trait originated in a common ancestor and was lost in some lineages.

Natural diversity in the predatory behavior facilitates the establishment of a new robust model strain for nematode-trapping fungi

The paper identifies a highly responsive Arthrobotrys oligospora strain for studying fungal-nematode interactions and shows G-protein signaling is essential for trap formation.

Stout camphor tree genome fills gaps in understanding of flowering plant genome and gene family evolution

The paper presents the first genome assembly of the stout camphor tree, revealing evolutionary insights into flowering plant genomes and gene family evolution.

Comparative genomics of the major parasitic worms

This paper compares genomes of 81 nematode and platyhelminth species to identify gene families related to parasitism and prioritize new drug targets.

Inferring synteny between genome assemblies: a systematic evaluation

The paper evaluates how draft genome assemblies affect synteny analysis and finds that fragmented assemblies can lead to significant underestimation of synteny and unreliable downstream results.

Comparative and population genomics landscape of Phellinus noxius: a hypervariable fungus causing root rot in trees

This study uses comparative and population genomics to analyze Phellinus noxius, revealing its genetic diversity, mating system, and evolutionary patterns.