Biology subjects

Kawaguchi, Y. W.

Publications and source records attributed to Kawaguchi, Y. W..

6 recordsLinked to original sources

bioRxiv2026

From photoprotection to growth: shifts in high-light acclimation strategies associated with molecular evolutionary rates in duckweeds

Molecular evolutionary rates vary widely among lineages, yet the biological processes generating this variation remain poorly understood. In plants, which lack an early-segregated germline, growth- and environment-dependent physiology could itself influence mutation accumulation and, ultimately, substitution rates. Here we examine this possibility in duckweeds (Araceae, Lemnoideae), whose closely related lineages differ severalfold in sequence divergence. Nonsynonymous and synonymous divergence scaled proportionally across all six lineages examined, indicating that this heterogeneity does not reflect differences in selective constraint and instead points to variation in mutation rate. Lineages without prominent anthocyanin accumulation occupied lower latitudes and, under high light, sustained higher relative growth rates and higher photosynthetic efficiency. Comparing the early-diverging, anthocyanin-accumulating Spirodela polyrhiza with the late-diverging, anthocyanin-free Wolffia australiana revealed contrasting acclimation strategies: S. polyrhiza preferentially induced photoprotective pathways, including anthocyanin biosynthesis and non-photochemical quenching, whereas W. australiana instead expanded mitochondrial oxidative phosphorylation together with the cytosolic translational machinery, and broadly remodeled primary metabolism. Duckweed lineages therefore differ in how they balance photoprotection against photochemical energy use and downstream metabolic capacity, a divergence that may be associated with their lineage-specific molecular evolutionary rates.

evolutionary biology↗

bioRxiv2026

Shark sexing from forensic, archival, and developmental samples using sex-linked DNA markers

The effective management of threatened shark populations relies on accurate demographic data, particularly operational sex ratios. While sex identification in intact shark bodies is straightforward through the presence of external male organs, namely claspers, it remains impossible for processed fins in the illegal wildlife trade, early-stage embryos in breeding programs, or archived tissue fragments and blood samples where morphological traits are lost. Here, we present a robust molecular sexing framework leveraging recently identified sequences from shark sex chromosomes, consistently organized in the XY system, to our current knowledge. Our approach consists of two distinct methodologies tailored to the the current identification status of sex chromosome sequences in the target species. For the whale shark Rhincodon typus and the brownbanded bamboo shark Chiloscyllium punctatum, we employed end-point PCR assays targeting male-specific Y-linked markers. For the cloudy catshark Scyliorhinus torazame, we developed a quantitative PCR (qPCR) assay targeting differential X chromosome dosage. In this dosage-based system, females (XX) are distinguished by an amplification profile approximately one cycle earlier than males (XY). By integrating X-linked dosage quantification, our framework provides a critical internal control that significantly enhances reliability, allowing researchers to distinguish true females from PCR failures. This toolkit offers a versatile solution for diverse applications, ranging from the study of sex determination mechanisms in pre-phenotypic embryos to the reconstruction of sex ratios from space-constrained tissue archives and global wildlife forensics, thereby contributing to the comprehensive conservation of shark biodiversity.

ecology↗

bioRxiv2025

Improved genome assembly of whale shark, the world's biggest fish: revealing "chromocline" in intragenomic heterogeneity

High-quality chromosome-level assemblies are essential for understanding genome evolution but remain difficult to obtain for large and complex genomes. Here we present a near gap-free genome assembly of the whale shark (Rhincodon typus) generated with long-read sequencing and Hi-C scaffolding, markedly improving contiguity and completeness. In particular, the X chromosome was extended to nearly twice its previous length, and putative pseudoautosomal regions were identified. Moreover, we report the first Y-linked scaffolds for this species. Comparative analyses with the zebra shark revealed exceptionally low substitution rates across the genome. We further detected a negative correlation between chromosome length and synonymous substitution rate (dS), explained by a positional gradient, designated as "chromocline", in which substitution rates gradually decrease from chromosomal ends toward central regions. Notably, the X chromosome exhibited low dS compared with autosomes of similar size, consistent with male-driven evolution. Our results highlight positional and sex-chromosome effects as key determinants of molecular evolutionary rates. The improved assembly will enable broad application to population-genetic and conservation genomic analyses in the whale shark.

evolutionary biology↗

bioRxiv2024

A single episode of sexual reproduction can prevent population extinction under multiple stressors

Recent studies have shown that organisms can adapt to changing environments through rapid contemporary evolution. Although intraspecific genetic variation is necessary for rapid evolution to occur, little is known how genetic variation has been produced and maintained before rapid evolution. Here we show that a single episode of sexual reproduction can produce a large amount of intraspecific trait variation that allows population growth in degraded environments by laboratory experiments of a green alga, Closterium peracerosum-strigosum-littorale complex. We observed population dynamics of the alga under multiple stressors and confirmed that high salinity and low pH decreased population growth rates. By comparing parental and their hybrid F1 populations, we observed larger variation in population growth rates of F1 populations (i.e., transgressive segregation) when pH was low. Interestingly, even when parental populations had negative growth rates, some F1 populations showed positive growth rates in severe environmental conditions due to the large variation in population growth. By utilizing the recently obtained genomic information of the alga, we found greater enrichment of genes with copy number variations in terms related to pH stress than those to salt stress in a gene ontology (GO) enrichment analysis. Our results suggest that recombination and variation in the number of gene copies might produce large genetic variation in the F1 generation. This will be an important step toward a better understanding of evolutionary rescue, where rapid evolution prevents population extinction in changing environments.

evolutionary biology↗

bioRxiv2023

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than twofold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.

evolutionary biology↗

bioRxiv2023

Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (desmidiales, zygnematophyceae, streptophyta)

Members of the Closterium peracerosum-strigosum-littorale (C. psl.) complex are unicellular zygnematophycean algae, which are suggested to be closely related to land plants. A zygospore is typically formed as a result of conjugation between mating-type plus (mt+) and mating-type minus (mt-) cells during sexual reproduction in heterothallic strains. On the other hand, zygospores are formed between genetically identical cells in homothallic strains. In this study, we isolated novel homothallic strains in the C. psl. complex. Phylogenetic analysis revealed the polyphyly of homothallic strains, suggesting multiple transitions between homothallism and heterothallism in the C. psl. complex. We measured the 1C genome size of the C. psl. complex by using flow cytometry after staining nuclei with propidium iodide, which ranged from 0.53 to 1.42 Gbp. We counted chromosome numbers using confocal microscope images, finding that two homothallic strains had fewer chromosomes than four heterothallic strains. Genome size positively correlated with both the cell size and chromosome number. Chromosome numbers differed even within the same mating group, suggesting a mechanism tolerating chromosomal rearrangements during meiosis in the C. psl. complex.

plant biology↗