University of the Ryukyus · Graduate School of Science and Engineering · 教授

Research keywordsRNA-Seq・chromatophores・Oryzias fishes・mitochondrial recombination・population structure・environmental DNA

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• A Simple Method for RNA-Seq of Manually Isolated Chromatophores in Oryzias Fishes.2026 · RNA sequencing (RNA-seq) has become an essential tool for analyzing gene expression and exploring cell type-specific transcriptomes. However, sample preparation and quality control remain challenging, as current approaches typically rely on dissecting tissues containing mixed cell populations or using flow cytometry to isolate fluorescently labeled cells. Here we present a simple and reliable method for RNA-seq of chromatophores (pigment cells) by manually isolating cells based on their natural pigmentation. We analyzed four chromatophore types-melanophores, xanthophores, iridophores, and leucophores-in medaka (Oryzias latipes). Remarkably, as few as 100 cells per type yielded reasonably high-quality transcriptomes sufficient to identify differentially expressed genes (DEGs). Furthermore, this method was successfully applied to a non-model medaka species, O. woworae, which shares the same four chromatophore types. Our approach enables efficient, low-cost, and cross-species transcriptome analysis of chromatophores without requiring transgenic markers or flow cytometry.
• Genetic and body-shape divergence of the ricefish Oryzias nigrimas between populations in Lake Poso and the outflowing Poso River, Sulawesi, Indonesia2026 · Ixchel F. Mandagi, Akira W. R. Masengi, Hirozumi Kobayashi, Handung Nuryadi, Kawilarang W. A. Masengi, Kazunori Yamahira, Ryo Kakioka
• Population structure of the western Indian endemic medaka, Oryzias setnai, inferred from mitochondrial haplotypes2025 · V. K. Anoop, Handung Nuryadi, Rajeev Raghavan, Kazunori Yamahira
• Shorter Recruitment Periods and Higher Fecundity in High-Latitude Populations of the Oryzias latipes Species Complex2025 · Shingo Fujimoto, Iki Murase, Hirozumi Kobayashi, Bayu K. A. Sumarto, Mitsuharu Yagi, Kazunori Yamahira

• 核ゲノムによるミトコンドリア家畜化維持機構の遺伝基盤と進化に関する研究2025 · 挑戦的研究(開拓)
• 異種由来ミトコンドリアによる新規種分化様式の検証2025 · 基盤研究(A)
• 熱帯の多様性創出における急速な性染色体置換の役割2021 · 基盤研究(A)

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