Biology subjects

Yen, H.-C.

Publications and source records attributed to Yen, H.-C..

3 recordsLinked to original sources

bioRxiv2026

Conserved RGF1 peptide signaling regulates root meristem development through ROS in Arabidopsis and rice

The root meristem is essential for stem cell maintenance and root development in plants. In Arabidopsis, Root meristem Growth Factor (RGF) peptides and their receptors regulate root meristem size through reactive oxygen species (ROS)-dependent signalling. RGF1-mediated ROS redistribution post-translationally stabilises the root meristem master regulator PLETHORA2 (PLT2). Although genomic studies suggest that RGF-receptor modules are evolutionarily conserved across land plants, their functional characterisation has remained largely limited to Arabidopsis. Here, we show that Oryza sativa RGF1-1 (OsRGF1-1) functions as a rice homologue of Arabidopsis RGF1 (AtRGF1). CRISPR/Cas9-generated Osrgf1-1 mutants exhibited shorter seminal roots, reduced root meristem size, and decreased superoxide (O2*-) accumulation. EdU staining further confirmed that cell proliferation activity was reduced in the Osrgf1-1 mutants. The Osrgf1-1 mutants were sensitive to low concentrations of chemically synthesised mature OsRGF1-1 peptide. This low dose of OsRGF1-1 peptide restored seminal root growth and O2*- accumulation in the Osrgf1-1 mutants but had no detectable effect on the wild type. Functional analyses using Arabidopsis rgfr receptor mutants further demonstrated that OsRGF1-1 is perceived through conserved RGF receptor machinery. Together, our findings provide the first functional evidence that the RGF1-receptor-ROS signalling module is evolutionarily conserved between dicots and monocots in the regulation of root meristem development.

plant biology↗

bioRxiv2024

Population genomics of a thermophilic cyanobacterium revealed divergence at subspecies level and possible adaptation genes

BackgroundCyanobacteria are diverse phototrophic microbes with ecological importance and potential for biotechnology applications. One species of thermophilic cyanobacteria, Thermosynechococcus taiwanensis, has been studied for biomass pyrolysis, estrogen degradation, and the production of bioethanol, monosaccharide, and phycocyanin. To better understand the diversity and evolution of this species, we sampled across different regions in Taiwan for strain isolation and genomic analysis. ResultsA total of 27 novel strains were isolated from nine of the 12 hot springs sampled and subjected to whole genome sequencing. Including strains studied previously, our genomic analyses encompassed 32 strains from 11 hot springs. Genome sizes among these strains ranged from 2.64 to 2.70 Mb, with an average of 2.66 Mb. Annotation revealed between 2,465 and 2,576 protein-coding genes per genome, averaging 2,537 genes. Core-genome phylogeny, gene flow estimates, and overall gene content divergence consistently supported the within-species divergence into two major populations. While isolation by distance partially explained the within-population divergence, the factors driving divergence between populations remain unclear. Nevertheless, this species likely has a closed pan-genome comprising approximately 3,030 genes, with our sampling providing sufficient coverage of its genomic diversity. To investigate the divergence and potential adaptations, we identified genomic regions with significantly lower nucleotide diversity, indicating loci that may have undergone selective sweeps within each population. We identified 149 and 289 genes within these regions in populations A and B, respectively. Only 16 genes were common to both populations, suggesting that selective sweeps primarily targeted different genes in the two populations. Key genes related to functions such as carbon fixation, photosynthesis, motility, and ion transport were highlighted. ConclusionsThis work provides a population genomics perspective on a hot spring cyanobacterial species in Taiwan. Beyond advancing our understanding of microbial genomics and evolution, the strains collected and genome sequences generated in this work provide valuable materials for future development and utilization of biological resources.

genomics↗

bioRxiv2024

Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes

Genome-based analysis allows for large-scale classification of diverse bacteria and has been widely adopted for delineating species. Unfortunately, for higher taxonomic ranks such as genus, establishing a generally accepted approach based on genome analysis is challenging. While core-genome phylogenies depict the evolutionary relationships among species, determining the correspondence between clades and genera may not be straightforward. For genotypic divergence, percentage of conserved proteins (POCP) and genome-wide average amino acid identity (AAI) are commonly used, but often do not provide a clear threshold for classification. In this work, we investigated the utility of global comparisons and data visualization in identifying clusters of species based on their overall gene content, and rationalized that such patterns can be integrated with phylogeny and other information such as phenotypes for improving taxonomy. As a proof of concept, we selected 177 representative genome sequences from the Mycoplasmatales-Entomoplasmatales clade within the class Mollicutes for a case study. We found that the clustering patterns corresponded to the current understanding of these organisms, namely the split into three above-genus groups: Hominis, Pneumoniae, and Spiroplasma-Entomoplasmataceae-Mycoides (SEM). However, at the genus level, several important issues were found. For example, recent taxonomic revisions that split the Hominis group into three genera and Entomoplasmataceae into five genera are problematic, as those newly described or emended genera lack clear differentiations in gene content from one another. Moreover, several cases of mis-classification were identified. These findings demonstrated the utility of this approach and the potential application for other bacteria. Impact statementTaxonomy provides a foundation for communication that involves biological entities. As such, robust classification and standardized nomenclature are critical. In recent years, genome analysis has been widely adopted for delineating species, but generally accepted approaches for delineating higher taxonomic ranks such as genus are lacking. In this work, we demonstrated that the comparison of overall gene content among species provides an intuitive method for identifying groups of similar organisms that can correspond to genera. Moreover, several critical issues were identified when we applied the method to evaluate recent taxonomic revisions that affected many pathogens with biomedical or economic importance. These findings serve as a cautionary tale against the over-reliance of core-genome centered approaches in taxonomy. Data SummaryThe 183 genome assemblies analyzed in this study were obtained from the National Center for Biotechnology Information (NCBI) Genome Database. The accession numbers are provided in Table S1.

genomics↗