1
|
Liang W, Xu Y, Cui X, Li C, Lu S. Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta. Int J Mol Sci 2024; 25:6043. [PMID: 38892231 PMCID: PMC11172604 DOI: 10.3390/ijms25116043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Aristolochia contorta Bunge is an academically and medicinally important plant species. It belongs to the magnoliids, with an uncertain phylogenetic position, and is one of the few plant species lacking a whole-genome duplication (WGD) event after the angiosperm-wide WGD. A. contorta has been an important traditional Chinese medicine material. Since it contains aristolochic acids (AAs), chemical compounds with nephrotoxity and carcinogenicity, the utilization of this plant has attracted widespread attention. Great efforts are being made to increase its bioactive compounds and reduce or completely remove toxic compounds. MicroRNAs (miRNAs) and natural antisense transcripts (NATs) are two classes of regulators potentially involved in metabolism regulation. Here, we report the identification and characterization of 223 miRNAs and 363 miRNA targets. The identified miRNAs include 51 known miRNAs belonging to 20 families and 172 novel miRNAs belonging to 107 families. A negative correlation between the expression of miRNAs and their targets was observed. In addition, we identified 441 A. contorta NATs and 560 NAT-sense transcript (ST) pairs, of which 12 NATs were targets of 13 miRNAs, forming 18 miRNA-NAT-ST modules. Various miRNAs and NATs potentially regulated secondary metabolism through the modes of miRNA-target gene-enzyme genes, NAT-STs, and NAT-miRNA-target gene-enzyme genes, suggesting the complexity of gene regulatory networks in A. contorta. The results lay a solid foundation for further manipulating the production of its bioactive and toxic compounds.
Collapse
Affiliation(s)
- Wenjing Liang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yayun Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xinyun Cui
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Caili Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shanfa Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| |
Collapse
|
2
|
Domínguez-Rosas E, Hernández-Oñate MÁ, Fernandez-Valverde SL, Tiznado-Hernández ME. Plant long non-coding RNAs: identification and analysis to unveil their physiological functions. FRONTIERS IN PLANT SCIENCE 2023; 14:1275399. [PMID: 38023843 PMCID: PMC10644886 DOI: 10.3389/fpls.2023.1275399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Eukaryotic genomes encode thousands of RNA molecules; however, only a minimal fraction is translated into proteins. Among the non-coding elements, long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. LncRNAs are associated mainly with the regulation of the expression of the genome; nonetheless, their study has just scratched the surface. This is somewhat due to the lack of widespread conservation at the sequence level, in addition to their relatively low and highly tissue-specific expression patterns, which makes their exploration challenging, especially in plant genomes where only a few of these molecules have been described completely. Recently published high-quality genomes of crop plants, along with new computational tools, are considered promising resources for studying these molecules in plants. This review briefly summarizes the characteristics of plant lncRNAs, their presence and conservation, the different protocols to find these elements, and the limitations of these protocols. Likewise, it describes their roles in different plant physiological phenomena. We believe that the study of lncRNAs can help to design strategies to reduce the negative effect of biotic and abiotic stresses on the yield of crop plants and, in the future, help create fruits and vegetables with improved nutritional content, higher amounts of compounds with positive effects on human health, better organoleptic characteristics, and fruits with a longer postharvest shelf life.
Collapse
Affiliation(s)
- Edmundo Domínguez-Rosas
- Coordinación de Tecnología de Alimentos de Origen Vegeta, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | | | | | - Martín Ernesto Tiznado-Hernández
- Coordinación de Tecnología de Alimentos de Origen Vegeta, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| |
Collapse
|
3
|
Wang C, Pan G, Lu X, Qi W. Phosphorus solubilizing microorganisms: potential promoters of agricultural and environmental engineering. Front Bioeng Biotechnol 2023; 11:1181078. [PMID: 37251561 PMCID: PMC10213388 DOI: 10.3389/fbioe.2023.1181078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Phosphate solubilizing microorganisms (PSMs) are known as bacteria or fungi that make insoluble phosphorus in soil available to plants. To date, as beneficial microbes, studies on PSMs indicated they have potential applications in agriculture, environmental engineering, bioremediation, and biotechnology. Currently high cost and competition from local microbe are the most important factors hindering PSMs commercialization and application as for instance biofertilizer, soil conditioner or remediation agent, etc. There are several technical strategies can be engaged to approach the solutions of these issues, for instance mass production, advance soil preparation, genetic engineering, etc. On the other hand, further studies are needed to improve the efficiency and effectiveness of PSMs in solubilizing phosphates, promoting plant growth, soil remediation preferably. Hopefully, PSMs are going to be developed into ecofriendly tools for sustainable agriculture, environment protection and management in the future.
Collapse
Affiliation(s)
- Chengdong Wang
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guojun Pan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Lu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs, Nanjing, China
| |
Collapse
|
4
|
He B, Hu F, Du H, Cheng J, Pang B, Chen X, Lv Y. Omics-driven crop potassium use efficiency breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:1076193. [PMID: 36507409 PMCID: PMC9730507 DOI: 10.3389/fpls.2022.1076193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/11/2022] [Indexed: 06/01/2023]
Affiliation(s)
- Bing He
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
5
|
Luo C, He B, Shi P, Xi J, Gui H, Pang B, Cheng J, Hu F, Chen X, Lv Y. Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:988845. [PMID: 36204077 PMCID: PMC9530330 DOI: 10.3389/fpls.2022.988845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2022] [Indexed: 06/01/2023]
Abstract
Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
Collapse
Affiliation(s)
- Chuping Luo
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pibiao Shi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinlong Xi
- Zhejiang Institute of Standardization, Hangzhou, China
| | - Hongbing Gui
- College of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Bingwen Pang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Cheng
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Yuanda Lv
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
6
|
Chen X, Wang C, He B, Wan Z, Zhao Y, Hu F, Lv Y. Transcriptome Profiling of Transposon-Derived Long Non-coding RNAs Response to Hormone in Strawberry Fruit Development. FRONTIERS IN PLANT SCIENCE 2022; 13:915569. [PMID: 35783970 PMCID: PMC9244616 DOI: 10.3389/fpls.2022.915569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/02/2022] [Indexed: 06/01/2023]
Abstract
Strawberry is an economically grown horticulture crop required for fruit consumption. The ripening of its fruit is a complex biological process regulated by various hormones. Abscisic acid (ABA) is a critical phytohormone involved in fruit ripening. However, little is known about the long non-coding RNAs (LncRNAs), especially transposon-derived LncRNA (TE-lncRNA), response to hormones during fruit ripening in octoploid strawberry. In the study, the transcriptome data of developing strawberry fruits treated with ABA and its inhibitor Nordihydroguaiaretic acid (NGDA) were analyzed to identify responsive LncRNAs and coding genes. A total of 14,552 LncRNAs were identified, including 8,617 transposon-derived LncRNAs (TE-LncRNAs), 412 LncRNAs (282 TE-LncRNAs), and 382 ABA-sensitive LncRNAs (231 TE-LncRNAs). Additionally, a weighted co-expression network analysis constructed 27 modules containing coding RNAs and LncRNAs. Seven modules, including "MEdarkorange" and "MElightyellow" were significantly correlated with ABA/NDGA treatments, resulting in 247 hub genes, including 21 transcription factors and 22 LncRNAs (15 TE-LncRNAs). Gene ontology enrichment analysis further revealed that ABA/NDGA-responsive modules, including LncRNAs, were associated with various metabolic pathways involved in strawberry fruit development and ripening, including lipid metabolism, organic acid metabolism, and phenylpropanoid metabolism. The current study identifies many high-confidence LncRNAs in strawberry, with a percentage of them being ABA pathway-specific and 22 hub-responsive LncRNAs, providing new insight into strawberry or other Rosaceae crop fruit ripening.
Collapse
Affiliation(s)
- Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forest, Zhenjiang, China
- Engineering and Technical Center for Modern Horticulture, Jurong, China
| | - Chengdong Wang
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zifan Wan
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forest, Zhenjiang, China
- Engineering and Technical Center for Modern Horticulture, Jurong, China
| | - Yukun Zhao
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forest, Zhenjiang, China
- Engineering and Technical Center for Modern Horticulture, Jurong, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|