| Multidimensional analysis of long noncoding RNAs function in Solanaceae plants | |
Yang, Wenjing1; Bai, Quanzi; Zhang, Xuan ; Chen, Wen2; Cai, Ankang1; Li, Jing; Gao, Xiaoyang; Yao, Baolin3; Liu, Jiazhi1,4,5; Li, Yan1; Chen, Jianghua; Liu, Changning
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| 2025 | |
| Source Publication | NEW PHYTOLOGIST
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| ISSN | 0028-646X |
| Volume | 247Issue:3Pages:1041-1059 |
| Abstract | Long noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially in the Solanaceae family. While substantial progress has been made in identifying lncRNAs in different Solanaceae species, systematic functional annotations are lacking. In this study, we uniformly identified and systematically characterized lncRNAs from seven Solanaceous species using large-scale strand-specific RNA-seq (ssRNA-seq). About 113 700 lncRNA genes were obtained and analyzed for their sequence, conservation, expression profile, epigenetic signals, and genetic mutants. In tomato, 97.4% of lncRNAs have been annotated with basic characteristics. Also, 25.7% of lncRNAs were further predicted to be involved in stress response, development, and metabolism. Comparisons between lncRNAs and protein-coding genes (PCGs) highlighted unique characteristics in tissue expression, stress responses, sequence composition, and epigenetic signal distribution. We shared our datasets on Solanaceous lncRNAs at . Taking fruit development and ripening as an example, we further mined the data resources and predicted a total of 1158 lncRNAs associated with this process, presenting how our curated data can be utilized to discover the functions of plant lncRNAs. Overall, this study provides a comprehensive multidimensional framework for lncRNA functional research, which serves as a valuable reference for understanding lncRNA functions in other plants. |
| Keyword | FRUIT-DEVELOPMENT EXPRESSION LNCRNAS TRANSCRIPTOME ARABIDOPSIS ANNOTATION PROFILES NETWORK GROWTH ROLES |
| Subject Area | Plant Sciences |
| DOI | 10.1111/nph.70261 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:001499856800001 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | https://ir.xtbg.ac.cn/handle/353005/14761 |
| Collection | 2012年后新成立研究组 |
| Affiliation | 1.Chinese Acad Sci, CAS Key Lab Trop Plant Resources & Sustainable Use, Yunnan Key Lab Crop Wild Relat Om, Xishuangbanna Trop Bot Garden,State Key Lab Plant, Kunming 650223, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Hunan Univ Chinese Med, Med Sch, Key Lab Vasc Biol & Translat Med, Changsha 410208, Peoples R China 4.Univ Sci & Technol China, Sch Life Sci, Hefei 230026, Peoples R China 5.Chinese Acad Sci, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 6.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Crop Wild Relat Om, Kunming 650201, Yunnan, Peoples R China |
| Recommended Citation GB/T 7714 | Yang, Wenjing,Bai, Quanzi,Zhang, Xuan,et al. Multidimensional analysis of long noncoding RNAs function in Solanaceae plants[J]. NEW PHYTOLOGIST,2025,247(3):1041-1059. |
| APA | Yang, Wenjing.,Bai, Quanzi.,Zhang, Xuan.,Chen, Wen.,Cai, Ankang.,...&Liu, Changning.(2025).Multidimensional analysis of long noncoding RNAs function in Solanaceae plants.NEW PHYTOLOGIST,247(3),1041-1059. |
| MLA | Yang, Wenjing,et al."Multidimensional analysis of long noncoding RNAs function in Solanaceae plants".NEW PHYTOLOGIST 247.3(2025):1041-1059. |
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| Multidimensional ana（4116KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Download | |
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