Biology subjects

Yoshitake, K.

Publications and source records attributed to Yoshitake, K..

24 records · Page 2Linked to original sources

bioRxiv2021

Mutations in a β-group of solute carrier gene are responsible for egg and eye coloration of the brown egg 4 (b-4) mutant in the silkworm, Bombyx mori

The brown egg 4 (b-4) is a recessive mutant in the silkworm (Bombyx mori), whose egg and adult compound eyes exhibit a reddish-brown color instead of normal purple and black, respectively. By double digest restriction-site associated DNA sequencing (ddRAD-seq) analysis, we narrowed down a region linked to the b-4 phenotype to approximately 1.1 Mb that contains 69 predicted gene models. RNA-seq analysis in a b-4 strain indicated that one of the candidate genes had a different transcription start site, which generates a short open reading frame. We also found that exon skipping was induced in the same gene due to an insertion of a transposable element in other two b-4 mutant strains. This gene encoded a putative amino acid transporter that belongs to the {beta}-group of solute carrier (SLC) family and is orthologous to Drosophila eye color mutant gene, mahogany (mah). Accordingly, we named this gene Bmmah. We performed CRISPR/Cas9-mediated gene knockout targeting Bmmah. Several adult moths in generation 0 (G0) had totally or partially reddish-brown compound eyes. We also established three Bmmah knockout strains, all of which exhibit reddish-brown eggs and adult compound eyes. Furthermore, eggs from complementation crosses between the b-4 mutants and the Bmmah knockout mutants also exhibited reddish-brown color, which was similar to the b-4 mutant eggs, indicating that Bmmah is responsible for the b-4 phenotypes. HighlightO_LIResponsible region for the brown egg 4 (b-4) mutation was narrowed down by double digest restriction-site associated DNA sequencing (ddRAD-seq). C_LIO_LIThe gene structure was disrupted in one of the candidate genes, Bombyx mori mahogany (Bmmah), in the b-4 mutant strains. C_LIO_LICRISPR/Cas9-mediated gene knockout and complementation test confirmed that the Bmmah is responsible for the b-4 phenotypes. C_LIO_LIThe Bmmah encoded a putative amino acid transporter that belongs to the {beta}-group of solute carrier family. C_LIO_LIThe Bmmah gene is essential for normal colorization of eggs, compound eyes, and ganglions. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/436376v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@10d1d56org.highwire.dtl.DTLVardef@12df5org.highwire.dtl.DTLVardef@1703701org.highwire.dtl.DTLVardef@2b5bcf_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

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

PIWI/piRNA suppress transposon activity in animals, thereby safeguarding the genome from detrimental insertion mutagenesis. Recently, evidence revealed additional piRNA targets and functions in various animals. Although piRNAs are ubiquitously expressed in somatic tissues of the pearl oyster Pinctada fucata, their role is not well-characterized. Here, we report a PIWI/piRNA pathway, including piRNA biogenesis and piRNA-mediated gene regulation in P. fucata. A locked-nucleic-acid modified oligonucleotide (LNA-antagonist) was used to silence a single piRNA (piRNA0001) expression in P. fucata, which resulted in the differential expression of hundreds of endogenous genes. Target prediction analysis revealed that, following silencing, tens of endogenous genes were targeted by piRNA0001, including twelve up-regulated and nine down-regulated genes. Bioinformatic analyses suggested that different piRNA populations participate in the ping-pong amplification loop in a tissue-specific manner. These findings have improved our knowledge of the role of piRNA in mollusks, and provided evidence to understand the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germline cells.

molecular biology↗

bioRxiv2020

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

The presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm from Gasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome of Gasterosteus nipponicus sequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.

genomics↗

bioRxiv2018

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

BackgroundAging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.\n\nResultsScreening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation of hmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle and atf3 in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.\n\nConclusionsOur results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.

bioinformatics↗

bioRxiv2018

Designed hybrids facilitate efficient generation of high-resolution linkage maps

In sequencing eukaryotic genomes, linkage maps are indispensable for building scaffolds with which to assemble and/or to validate chromosomes. However, current approaches to construct linkage maps are limited by marker density and cost-effectiveness, especially for wild organisms. We have now devised a new strategy based on artificially generated hybrid organisms to acquire ultra high-density genomic markers at lower cost and build highly accurate linkage maps. Using this method, linkage maps and draft sequences for two species of pufferfish were obtained simultaneously. We anticipate that the method will accelerate genomic analysis of sexually reproducing organisms.

genomics↗

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↗