Shuichi Asakawa

Omitting end preparation reduces index misassignment in Nanopore-based DNA metabarcoding: application to a decadal coastal time series in the Sea of Okhotsk

The paper develops a workflow to reduce index misassignment in Nanopore-based eDNA metabarcoding, applied to a decadal coastal time series showing seasonal fish taxa patterns.

The minimal endosymbiosis between Spurilla braziliana (Aeolidiidae, Nudibranchia) and Symbiodiniaceae

This study examines the algal symbiosis in Spurilla braziliana, finding limited morphological adaptations and absence of associated bacteria, suggesting a primitive symbiotic state.

Environmental exosomes: Evidence of extracellular RNA release by aquatic organisms

The paper identifies that pearl oysters release exosomes containing species-specific RNA into the environment, suggesting a new role for aquatic exosomes in inter-organismal communication and ecological monitoring.

The Greenland shark genome: insights into deep-sea ecology and lifespan extremes

This paper presents the first chromosome-level genome assembly of the Greenland shark, identifying genetic features associated with its extreme longevity and deep-sea adaptations.

The complete mitochondrial genome of Spurilla braziliana MacFarland 1909 (Nudibranchia, Aeolidiidae).

This study sequenced and analyzed the complete mitochondrial genome of Spurilla braziliana, revealing its phylogenetic placement within the Aeolidioidea superfamily.

Estimating gross transcription rates from RNA level fluctuation data and the effects of sampling time intervals

This study develops an algorithm to estimate gross transcription rates from RNA level fluctuation data and examines how sampling time intervals affect these estimates.

Telomere-to-telomere genome assembly of matsutake (Tricholoma matsutake)

The paper presents the first telomere-to-telomere genome assembly of matsutake, revealing genomic features and variations that provide a reference for future genetic and conservation studies.

Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging

This study compares age-associated transcriptome changes in zebrafish and rat to identify common and species-specific aging features.

A model explaining mRNA level fluctuations based on activity demands and RNA age

The paper develops a model to explain mRNA level fluctuations by considering activity demands and RNA age, using single-cell time-series data to estimate transcription and degradation rates.

Zebrafish Danio rerio trunk muscle structure and growth from a spatial transcriptomics perspective

This study uses spatial transcriptomics to analyze zebrafish trunk muscle structure and growth, identifying spatial gene expression patterns and developmental processes in different muscle types.

Potential silencing of gene expression by PIWI-interacting RNAs (piRNAs) in somatic tissues in mollusk

The paper investigates the role of PIWI/piRNA in somatic tissues of the pearl oyster Pinctada fucata, showing that piRNA0001 regulates hundreds of endogenous genes through differential expression.

Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms

The paper constructs a chromosome-level genome of Gasterosteus nipponicus using ultra-dense linkage analysis from single-cell sperm sequencing data.

Designed hybrids facilitate efficient generation of high-resolution linkage maps

This paper introduces a method using hybrid organisms to generate high-resolution linkage maps at lower cost and higher density for pufferfish species.