Biology subjects

Iwasaki, W.

Publications and source records attributed to Iwasaki, W..

25 records · Page 2Linked to original sources

bioRxiv2021

Exploring dimensions of biodiversity in Japanese ferns

PremiseBiodiversity is often only measured with species richness. However, this ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. MethodsWe compiled a community dataset of 1,239 20 km x 20 km grid-cells including 672 taxa based on > 300,000 specimen records. We combined this with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity, and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid-cells with conservation zones and range maps of native Japanese deer. ResultsTaxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid-cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid-cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. ConclusionsOur integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple multiple metrics when establishing conservation priorities.

evolutionary biology↗

bioRxiv2021

Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

Chromosome folding links genome structure with gene function by generating distinct nuclear compartments and topologically associating domains (TADs). In mammals, these undergo preferential interactions and regulate gene expression. However, their role in fungal genome biology is unclear. Here, we combine Nanopore (ONT) sequencing with chromatin conformation capture sequencing (Hi-C) to reveal chromosome and epigenetic diversity in a group of obligate plant symbionts; the arbuscular mycorrhizal fungi (AMF). We find that five phylogenetically distinct strains of the model AMF Rhizophagus irregularis carry 33 chromosomes with substantial within species variability in size, as well as in gene and repeat content. Strain-specific Hi-C contact maps all reveal a checkerboard pattern that underline two dominant euchromatin (A) and heterochromatin (B) compartments. Each compartment differs in the level of gene transcription, regulation of candidate effectors and methylation frequencies. The A-compartment is more gene-dense and contains most core genes, while the B-compartment is more repeat-rich and has higher rates of chromosomal rearrangement. While the B-compartment is transcriptionally repressed, it has significantly more secreted proteins and in planta up-regulated candidate effectors, suggesting a possible host-induced change in chromosome conformation. Overall, this study provides a fine-scale view into the genome biology and evolution of prominent plant symbionts, and opens avenues to study the epigenetic mechanisms that modify chromosome folding during host-microbe interactions.

genomics↗

bioRxiv2020

Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model

Reconstruction of gene-content evolutionary history is an essential approach for understanding how complex biological systems have been organized. However, the existing gene-content evolutionary models cannot formulate complex and heterogeneous gene gain/loss processes, which reflect diverse evolutionary events and greatly depend on gene families. In this study, we developed Mirage (MIxture model with a Realistic evolutionary rate model for Ancestral Genome Estimation), which allows different gene families to have flexible gene gain/loss rates, but reasonably limits the number of parameters to be estimated by the expectation-maximization algorithm. Simulation analysis showed that Mirage can accurately estimate complex and heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history. Application to empirical datasets demonstrated that our evolutionary model better fits genome data from various taxonomic groups than other models. Using Mirage, we revealed that gene families of metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated. The source code of Mirage is freely available at https://github.com/fukunagatsu/Mirage.

bioinformatics↗

bioRxiv2018

Metaepigenomic analysis reveals the unexplored diversity of DNA methylations in an environmental prokaryotic community

DNA methylation plays important roles in prokaryotes, such as in defense mechanisms against phage infection, and the corresponding genomic landscapes--prokaryotic epigenomes--have recently begun to be disclosed. However, our knowledge of prokaryote methylation systems has been severely limited to those of culturable prokaryotes, whereas environmental communities are in fact dominated by uncultured members that must harbor much more diverse DNA methyltransferases. Here, using single-molecule real-time and circular consensus sequencing techniques, we revealed the metaepigenomes of an environmental prokaryotic community in the largest lake in Japan, Lake Biwa. A total of 19 draft genomes from phylogenetically diverse groups, most of which are yet to be cultured, were successfully reconstructed. The analysis of DNA chemical modifications identified 29 methylated motifs in those genomes, among which 14 motifs were novel.\n\nFurthermore, we searched for the methyltransferase genes responsible for the methylation of the detected novel motifs and confirmed their catalytic specificities via transformation experiments involving artificially synthesized genes. Finally, we found that genomes without DNA methylation tended to exhibit higher phage infection levels than those with methylation. In summary, this study proves that metaepigenomics is a powerful approach for revealing the vast unexplored variety of prokaryotic DNA methylation systems in nature.

microbiology↗

bioRxiv2018

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

The reconstruction of ancestral scenarios is widely used to study the evolution of characters along a phylogenetic tree. In the likelihood framework one commonly uses the marginal posterior probabilities of the character states, and the joint reconstruction of the most likely scenario. Both approaches are somewhat unsatisfactory. Marginal reconstructions provide users with state probabilities, but these are difficult to interpret and visualize, while joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.\n\nWe propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts and the Brier criterion to associate each node in the tree to a set of likely states. A unique state is predicted in the tree regions with low uncertainty, while several states are predicted in the uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated to the same states and use graph visualization tools. The method is implemented in the PastML program and web server.\n\nThe results on simulated data consistently show the accuracy and robustness of the approach. The method is applied to large tree comprising 3,619 sequences from HIV-1M subtype C sampled worldwide, which is processed in a few minutes. Results are very convincing: we retrieve and visualize the main transmission routes of HIV-1C; we demonstrate that drug resistance mutations mostly emerge independently under treatment pressure, but some resistance clusters are found, corresponding to transmissions among untreated patients.

evolutionary biology↗

bioRxiv2017

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Birds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Il-lumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.

ecology↗

bioRxiv2017

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus ×- yedoensis 'Somei-yoshino' across the Japanese archipelago

Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the \"Ohanami Project\", to obtain environmental DNA samples from petal surfaces of Cerasus x yedoensis Somei-yoshino across the Japanese archipelago during spring 2015. C. x yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained across a wide distribution; this DNA likely originated from pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.

microbiology↗