An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways
Abstract Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome‐wide scale. A total...
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| Format: | Article |
| Language: | English |
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Wiley
2025-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20564 |
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| author | Xiaoxia Ma Yinju Tang Zedi Feng Xiu Yin Yijun Meng Xiaopu Yin Tian Xie |
| author_facet | Xiaoxia Ma Yinju Tang Zedi Feng Xiu Yin Yijun Meng Xiaopu Yin Tian Xie |
| author_sort | Xiaoxia Ma |
| collection | DOAJ |
| description | Abstract Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome‐wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ‐specifically expressed, and 13 of these miRNAs could perform organ‐specific target regulation. More than 80% of the phasiRNA loci were organ‐specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ‐specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber‐specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme‐coding genes of the β‐elemene biosynthetic pathway showed that the downstream genes were tuber‐specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β‐elemene biosynthesis. Summarily, our report provided an organ‐specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant. |
| format | Article |
| id | doaj-art-7baaa13c7cbb4d5598c07c152a7925ed |
| institution | OA Journals |
| issn | 1940-3372 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
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| series | The Plant Genome |
| spelling | doaj-art-7baaa13c7cbb4d5598c07c152a7925ed2025-08-20T01:50:07ZengWileyThe Plant Genome1940-33722025-03-01181n/an/a10.1002/tpg2.20564An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathwaysXiaoxia Ma0Yinju Tang1Zedi Feng2Xiu Yin3Yijun Meng4Xiaopu Yin5Tian Xie6School of Pharmacy Hangzhou Normal University Hangzhou ChinaCollege of Life and Environmental Sciences Hangzhou Normal University Hangzhou ChinaCollege of Life and Environmental Sciences Hangzhou Normal University Hangzhou ChinaSchool of Pharmacy Hangzhou Normal University Hangzhou ChinaCollege of Life and Environmental Sciences Hangzhou Normal University Hangzhou ChinaSchool of Pharmacy Hangzhou Normal University Hangzhou ChinaSchool of Pharmacy Hangzhou Normal University Hangzhou ChinaAbstract Curcuma wenyujin Y. H. Chen et C. Ling (C. wenyujin) is a medicinal plant widely used for clinical treatments. In this study, integrated omics data analyses enabled us to discover the microRNAs (miRNAs) and the phased small interfering RNAs (phasiRNAs) on a transcriptome‐wide scale. A total of 186 mature miRNAs and 23 precursors were reported. Besides, 31 miRNAs of 14 families were organ‐specifically expressed, and 13 of these miRNAs could perform organ‐specific target regulation. More than 80% of the phasiRNA loci were organ‐specifically expressed, especially in tubers. In some cases, phasiRNAs with distinct increments, but with accordant organ‐specific expression patterns, were generated from a highly overlapped region, indicating that different machineries might be synchronously engaged in phasiRNA processing. Based on the transcriptome assembly, 28 and 56 tuber‐specific genes were identified to be involved in alkaloid and terpenoid metabolisms, respectively. Analysis of the enzyme‐coding genes of the β‐elemene biosynthetic pathway showed that the downstream genes were tuber‐specific, while the upstream genes were not. We assumed that the precursor metabolites produced in the other organs might be delivered to the tubers for the final steps of β‐elemene biosynthesis. Summarily, our report provided an organ‐specific transcriptome atlas of C. wenyujin, which could serve as the basis for the molecular studies on organ development and secondary metabolisms in this plant.https://doi.org/10.1002/tpg2.20564 |
| spellingShingle | Xiaoxia Ma Yinju Tang Zedi Feng Xiu Yin Yijun Meng Xiaopu Yin Tian Xie An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways The Plant Genome |
| title | An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways |
| title_full | An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways |
| title_fullStr | An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways |
| title_full_unstemmed | An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways |
| title_short | An organ‐specific transcriptome atlas of Curcuma wenyujin: MicroRNAs, phasiRNAs, and metabolic pathways |
| title_sort | organ specific transcriptome atlas of curcuma wenyujin micrornas phasirnas and metabolic pathways |
| url | https://doi.org/10.1002/tpg2.20564 |
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