MedakaBase as a unified genomic resource platform for medaka fish biology.
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| Format: | Artículo científico |
| Sprache: | en |
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DNA research : an international journal for rapid publication of reports on genes and genomes
2025
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| author | Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro |
| author_facet | Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro |
| collection | PubMed - marine biology |
| contents | MedakaBase as a unified genomic resource platform for medaka fish biology. Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro Animals Oryzias Databases, Genetic Genomics Genome Transcriptome Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3' untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase. |
| format | Artículo científico |
| id | pubmed_41122912 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | DNA research : an international journal for rapid publication of reports on genes and genomes |
| record_format | pubmed |
| spellingShingle | MedakaBase as a unified genomic resource platform for medaka fish biology. Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro Animals Oryzias Databases, Genetic Genomics Genome Transcriptome MedakaBase as a unified genomic resource platform for medaka fish biology. Morikami, Kenji Tanizawa, Yasuhiro Yagura, Masaru Sakamoto, Mika Kawamoto, Shoko Nakamura, Yasukazu Yamaguchi, Katsushi Shigenobu, Shuji Naruse, Kiyoshi Ansai, Satoshi Kuraku, Shigehiro Animals Oryzias Databases, Genetic Genomics Genome Transcriptome Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3' untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase. |
| title | MedakaBase as a unified genomic resource platform for medaka fish biology. |
| topic | Animals Oryzias Databases, Genetic Genomics Genome Transcriptome |
| url | https://pubmed.ncbi.nlm.nih.gov/41122912/ |