Biology subjects

Zhang, W.-C.

Publications and source records attributed to Zhang, W.-C..

3 recordsLinked to original sources

bioRxiv2026

Schizosaccharomyces orthogroup (SOG) resource: a web platform for exploring gene conservation in fission yeasts

The fission yeast Schizosaccharomyces pombe is a prominent model organism widely used to investigate fundamental cellular mechanisms. In addition to S. pombe, the genus Schizosaccharomyces includes six other species--S. octosporus, S. japonicus, S. cryophilus, S. osmophilus, S. lindneri, and S. versatilis. These fission yeast species share a common ancestor from which the genus diversified over more than 200 million years. This extensive evolutionary divergence provides opportunities for comparative genomics. Here, we present the Schizosaccharomyces orthogroup (SOG) resource, a web platform developed from our high-quality genome assemblies, gene annotations, and orthology assignments. Most fission yeast genes are assigned to one of over 5,000 orthogroups. The platform enables users to visualize orthogroup sequence alignments and phylogenetic trees, retrieve coding and flanking sequences, and explore the conservation of local synteny. This resource will benefit researchers focusing on individual genes as well as those investigating gene evolution at broader scales. It is freely accessible at https://www.sogweb.org. TAKE AWAYO_LIThe SOG resource covers all known species of Schizosaccharomyces. C_LIO_LIThe platform is built on high-quality genome assemblies and annotations. C_LIO_LIMost genes are assigned to one of over 5,000 orthogroups. C_LIO_LIUsers can view and explore alignments, phylogenetic trees, and local synteny. C_LIO_LIThis free resource aids functional and evolutionary research. C_LI

genomics↗

bioRxiv2025

Evolutionary persistence and divergence of the tdk killer meiotic driver family

Killer meiotic drivers (KMDs) are selfish genetic elements that achieve super-Mendelian inheritance by selectively eliminating gametes lacking the driver. Although predicted to arise recurrently, KMDs are generally considered evolutionarily ephemeral--going extinct after fixation or host suppression. The identification of tdk1, a single-gene KMD in the fission yeast Schizosaccharomyces pombe, provides a model for studying KMD evolution. Here, we identify two divergent tdk1 homologs (tdk210 and tdk203) from S. cryophilus, a fission yeast species that diverged [~]100 million years ago from S. pombe, as active KMDs. These three KMDs all act via post-germination killing, disrupting chromosome segregation in noncarrier progeny. Notably, they also exhibit striking functional divergences: tdk1, tdk210, and tdk203 are mutually incompatible (showing no cross-resistance), and the latter two act independently of Bdf1/Bdf2--host chromatin proteins required for tdk1 killing. Phylogenetic analyses of the dozens of tdk family genes in Schizosaccharomyces support long-term persistence and rapid evolutionary dynamics of this gene family. Remarkably, homologs in distantly related fungal phyla display genomic and structural similarities to Schizosaccharomyces tdk genes, suggesting a deeply rooted origin of this KMD family in fungi. Our findings reveal that a single KMD family can undergo repeated functional innovation--generating mutually incompatible variants and rewiring host dependencies--while maintaining a conserved killing mode over deep evolutionary time.

evolutionary biology↗

bioRxiv2022

A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus

Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and three other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these two species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of two types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of two types of mitochondrial selfish elements.

genomics↗