Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour.
<i>Amomum villosum</i> Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challen...
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2025-07-01
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| author | Yating Zhu Shuang Li Hongyou Zhao Qianxia Li Yanfang Wang Chunyong Yang Ge Li Yanqian Wang Lixia Zhang |
| author_facet | Yating Zhu Shuang Li Hongyou Zhao Qianxia Li Yanfang Wang Chunyong Yang Ge Li Yanqian Wang Lixia Zhang |
| author_sort | Yating Zhu |
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| description | <i>Amomum villosum</i> Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s sustainable development. Our research team observed a distinct premature fruiting phenomenon in <i>A. villosum</i>. We investigated the regulatory mechanisms underlying premature fruiting in <i>A. villosum</i> by identifying the key differentially expressed genes (DEGs) and metabolic pathways governing the premature fruiting (Precocious) and typical plants (CK) of the ‘Yunsha No.8’ cultivar. Transcriptomic sequencing (RNA-seq) and bioinformatic analyses were performed using the DNBSEQ<sup>TM</sup> platform. The sequencing generated 29.0 gigabases (Gb) of clean data, and 115,965 unigenes were identified, with an average length of 1368 bp. Based on the sequencing results, 1545 DEGs were identified. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were annotated for these DEGs. This study identifies phytohormone signaling, carbohydrate and lipid metabolism, and polysaccharide degradation as critical pathways controlling premature fruiting in <i>A. villosum</i>. Six randomly selected DEGs were validated using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), and the results corroborated the transcriptome data, confirming their reliability. This study lays the foundation for the elucidation of the molecular mechanisms and metabolic pathways driving premature fruiting in <i>A. villosum</i>. |
| format | Article |
| id | doaj-art-1f979454d8244cc6b2dfbbd1e282146a |
| institution | DOAJ |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj-art-1f979454d8244cc6b2dfbbd1e282146a2025-08-20T03:13:39ZengMDPI AGBiology2079-77372025-07-0114788310.3390/biology14070883Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour.Yating Zhu0Shuang Li1Hongyou Zhao2Qianxia Li3Yanfang Wang4Chunyong Yang5Ge Li6Yanqian Wang7Lixia Zhang8Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, ChinaYunnan Key Laboratory of Southern Medicinal Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China<i>Amomum villosum</i> Lour., a perennial medicinal plant in the Zingiber genus, usually requires approximately 3–4 years of vegetative growth from seed germination to first fruiting, resulting in high initial investment costs and a prolonged revenue cycle, which pose significant challenges to the industry’s sustainable development. Our research team observed a distinct premature fruiting phenomenon in <i>A. villosum</i>. We investigated the regulatory mechanisms underlying premature fruiting in <i>A. villosum</i> by identifying the key differentially expressed genes (DEGs) and metabolic pathways governing the premature fruiting (Precocious) and typical plants (CK) of the ‘Yunsha No.8’ cultivar. Transcriptomic sequencing (RNA-seq) and bioinformatic analyses were performed using the DNBSEQ<sup>TM</sup> platform. The sequencing generated 29.0 gigabases (Gb) of clean data, and 115,965 unigenes were identified, with an average length of 1368 bp. Based on the sequencing results, 1545 DEGs were identified. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were annotated for these DEGs. This study identifies phytohormone signaling, carbohydrate and lipid metabolism, and polysaccharide degradation as critical pathways controlling premature fruiting in <i>A. villosum</i>. Six randomly selected DEGs were validated using real-time fluorescence quantitative polymerase chain reaction (RT-qPCR), and the results corroborated the transcriptome data, confirming their reliability. This study lays the foundation for the elucidation of the molecular mechanisms and metabolic pathways driving premature fruiting in <i>A. villosum</i>.https://www.mdpi.com/2079-7737/14/7/883<i>Amomum villosum</i> Lour.premature fruitingRNA-seqdifferentially expressed gene |
| spellingShingle | Yating Zhu Shuang Li Hongyou Zhao Qianxia Li Yanfang Wang Chunyong Yang Ge Li Yanqian Wang Lixia Zhang Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. Biology <i>Amomum villosum</i> Lour. premature fruiting RNA-seq differentially expressed gene |
| title | Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. |
| title_full | Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. |
| title_fullStr | Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. |
| title_full_unstemmed | Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. |
| title_short | Transcriptome Sequencing-Based Analysis of Premature Fruiting in <i>Amomum villosum</i> Lour. |
| title_sort | transcriptome sequencing based analysis of premature fruiting in i amomum villosum i lour |
| topic | <i>Amomum villosum</i> Lour. premature fruiting RNA-seq differentially expressed gene |
| url | https://www.mdpi.com/2079-7737/14/7/883 |
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