Multiomics-based assessment of the impact of airflow on diverse plant callus cultures
Abstract Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, the interplay between cellular diversity and ambient conditions influences the metabolism of cultured tissues; understanding these fa...
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| Format: | Article |
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Nature Portfolio
2025-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04518-7 |
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| author | June-Sik Kim Muneo Sato Mikiko Kojima Muchamad Imam Asrori Yukiko Uehara-Yamaguchi Yumiko Takebayashi Thi Nhung Do Thi Yen Do Kieu Oanh Nguyen Thi Hitoshi Sakakibara Keiichi Mochida Shinjiro Ogita Masami Yokota Hirai |
| author_facet | June-Sik Kim Muneo Sato Mikiko Kojima Muchamad Imam Asrori Yukiko Uehara-Yamaguchi Yumiko Takebayashi Thi Nhung Do Thi Yen Do Kieu Oanh Nguyen Thi Hitoshi Sakakibara Keiichi Mochida Shinjiro Ogita Masami Yokota Hirai |
| author_sort | June-Sik Kim |
| collection | DOAJ |
| description | Abstract Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, the interplay between cellular diversity and ambient conditions influences the metabolism of cultured tissues; understanding these factors in detail will inform efforts to optimize culture conditions. This study presents multiomics datasets from callus cultures of tobacco (Nicotiana tabacum), rice (Oryza sativa), and two bamboo species (Phyllostachys nigra and P. bambusoides). Over four weeks, calli were cultured under continuous moisture without airflow or gradually reduced ambient moisture with airflow. For each sample, gene expression was profiled with high-throughput RNA sequencing, 442 metabolites were measured using liquid chromatography (LC) with triple-quadrupole mass spectrometry (LC–QqQMS), and 31 phytohormones were quantified using ultra-performance LC coupled with a tandem quadrupole mass spectrometer equipped with an electrospray interface (UPLC-ESI-qMS/MS) and ultra-high-performance LC–orbitrap MS (UHPLC-Orbitrap MS). These datasets highlight the impact of airflow on callus cultures, revealing differences between and within species, and provide a comprehensive resource to explore the physiology of callus growth. |
| format | Article |
| id | doaj-art-0a00e7cba43944fbbd5a3b56897a4317 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-0a00e7cba43944fbbd5a3b56897a43172025-02-09T12:11:39ZengNature PortfolioScientific Data2052-44632025-02-011211810.1038/s41597-025-04518-7Multiomics-based assessment of the impact of airflow on diverse plant callus culturesJune-Sik Kim0Muneo Sato1Mikiko Kojima2Muchamad Imam Asrori3Yukiko Uehara-Yamaguchi4Yumiko Takebayashi5Thi Nhung Do6Thi Yen Do7Kieu Oanh Nguyen Thi8Hitoshi Sakakibara9Keiichi Mochida10Shinjiro Ogita11Masami Yokota Hirai12RIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceProgram in Biological System Science, Graduate School of Comprehensive Scientific Research, Hiroshima Prefectural UniversityRIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceDepartment of Life Sciences, University of Science and Technology of Ha Noi, Vietnam Academy of Science and TechnologyRIKEN Center for Sustainable Resource ScienceRIKEN Center for Sustainable Resource ScienceProgram in Biological System Science, Graduate School of Comprehensive Scientific Research, Hiroshima Prefectural UniversityRIKEN Center for Sustainable Resource ScienceAbstract Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, the interplay between cellular diversity and ambient conditions influences the metabolism of cultured tissues; understanding these factors in detail will inform efforts to optimize culture conditions. This study presents multiomics datasets from callus cultures of tobacco (Nicotiana tabacum), rice (Oryza sativa), and two bamboo species (Phyllostachys nigra and P. bambusoides). Over four weeks, calli were cultured under continuous moisture without airflow or gradually reduced ambient moisture with airflow. For each sample, gene expression was profiled with high-throughput RNA sequencing, 442 metabolites were measured using liquid chromatography (LC) with triple-quadrupole mass spectrometry (LC–QqQMS), and 31 phytohormones were quantified using ultra-performance LC coupled with a tandem quadrupole mass spectrometer equipped with an electrospray interface (UPLC-ESI-qMS/MS) and ultra-high-performance LC–orbitrap MS (UHPLC-Orbitrap MS). These datasets highlight the impact of airflow on callus cultures, revealing differences between and within species, and provide a comprehensive resource to explore the physiology of callus growth.https://doi.org/10.1038/s41597-025-04518-7 |
| spellingShingle | June-Sik Kim Muneo Sato Mikiko Kojima Muchamad Imam Asrori Yukiko Uehara-Yamaguchi Yumiko Takebayashi Thi Nhung Do Thi Yen Do Kieu Oanh Nguyen Thi Hitoshi Sakakibara Keiichi Mochida Shinjiro Ogita Masami Yokota Hirai Multiomics-based assessment of the impact of airflow on diverse plant callus cultures Scientific Data |
| title | Multiomics-based assessment of the impact of airflow on diverse plant callus cultures |
| title_full | Multiomics-based assessment of the impact of airflow on diverse plant callus cultures |
| title_fullStr | Multiomics-based assessment of the impact of airflow on diverse plant callus cultures |
| title_full_unstemmed | Multiomics-based assessment of the impact of airflow on diverse plant callus cultures |
| title_short | Multiomics-based assessment of the impact of airflow on diverse plant callus cultures |
| title_sort | multiomics based assessment of the impact of airflow on diverse plant callus cultures |
| url | https://doi.org/10.1038/s41597-025-04518-7 |
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