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Numan M, Sun Y, Li G. Exploring the emerging role of long non-coding RNAs (lncRNAs) in plant biology: Functions, mechanisms of action, and future directions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108797. [PMID: 38850732 DOI: 10.1016/j.plaphy.2024.108797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA transcripts that surpass 200 nucleotides in length and lack discernible coding potential. LncRNAs that have been functionally characterized have pivotal functions in several plant processes, including the regulation of flowering, and development of lateral roots. It also plays a crucial role in the plant's response to abiotic stressors and exhibits vital activities in environmental adaptation. The progress in NGS (next-generation sequencing) and functional genomics technology has facilitated the discovery of lncRNA in plant species. This review is a brief explanation of lncRNA genomics, its molecular role, and the mechanism of action in plants. The review also addresses the challenges encountered in this field and highlights promising molecular and computational methodologies that can aid in the comparative and functional analysis of lncRNAs.
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Affiliation(s)
- Mian Numan
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Yuge Sun
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China.
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Liu T, Wu Q, Zhou S, Xia J, Yin W, Deng L, Song B, He T. Molecular Insights into the Accelerated Sprouting of and Apical Dominance Release in Potato Tubers Subjected to Post-Harvest Heat Stress. Int J Mol Sci 2024; 25:1699. [PMID: 38338975 PMCID: PMC10855572 DOI: 10.3390/ijms25031699] [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: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change-induced heat stress (HS) increasingly threatens potato (Solanum tuberosum L.) production by impacting tuberization and causing the premature sprouting of tubers grown during the hot season. However, the effects of post-harvest HS on tuber sprouting have yet to be explored. This study aims to investigate the effects of post-harvest HS on tuber sprouting and to explore the underlying transcriptomic changes in apical bud meristems. The results show that post-harvest HS facilitates potato tuber sprouting and negates apical dominance. A meticulous transcriptomic profiling of apical bud meristems unearthed a spectrum of differentially expressed genes (DEGs) activated in response to HS. During the heightened sprouting activity that occurred at 15-18 days of HS, the pathways associated with starch metabolism, photomorphogenesis, and circadian rhythm were predominantly suppressed, while those governing chromosome organization, steroid biosynthesis, and transcription factors were markedly enhanced. The critical DEGs encompassed the enzymes pivotal for starch metabolism, the genes central to gibberellin and brassinosteroid biosynthesis, and influential developmental transcription factors, such as SHORT VEGETATIVE PHASE, ASYMMETRIC LEAVES 1, SHOOT MERISTEMLESS, and MONOPTEROS. These findings suggest that HS orchestrates tuber sprouting through nuanced alterations in gene expression within the meristematic tissues, specifically influencing chromatin organization, hormonal biosynthesis pathways, and the transcription factors presiding over meristem fate determination. The present study provides novel insights into the intricate molecular mechanisms whereby post-harvest HS influences tuber sprouting. The findings have important implications for developing strategies to mitigate HS-induced tuber sprouting in the context of climate change.
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Affiliation(s)
- Tengfei Liu
- College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China;
| | - Qiaoyu Wu
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountainous Areas, Ministry of Agriculture and Rural Affairs, Guiyang 550025, China; (Q.W.); (S.Z.); (W.Y.); (L.D.)
| | - Shuai Zhou
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountainous Areas, Ministry of Agriculture and Rural Affairs, Guiyang 550025, China; (Q.W.); (S.Z.); (W.Y.); (L.D.)
| | - Junhui Xia
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Potato Engineering and Technology Research Center of Hubei Province, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (J.X.); (B.S.)
| | - Wang Yin
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountainous Areas, Ministry of Agriculture and Rural Affairs, Guiyang 550025, China; (Q.W.); (S.Z.); (W.Y.); (L.D.)
| | - Lujun Deng
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountainous Areas, Ministry of Agriculture and Rural Affairs, Guiyang 550025, China; (Q.W.); (S.Z.); (W.Y.); (L.D.)
| | - Botao Song
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Potato Engineering and Technology Research Center of Hubei Province, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (J.X.); (B.S.)
| | - Tianjiu He
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Agricultural Biotechnology, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountainous Areas, Ministry of Agriculture and Rural Affairs, Guiyang 550025, China; (Q.W.); (S.Z.); (W.Y.); (L.D.)
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Mazhar HSUD, Shafiq M, Ali H, Ashfaq M, Anwar A, Tabassum J, Ali Q, Jilani G, Awais M, Sahu R, Javed MA. Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum). Genes (Basel) 2023; 14:genes14040824. [PMID: 37107580 PMCID: PMC10137784 DOI: 10.3390/genes14040824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.
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Cao P, Zhan C, Yin J, Gong S, Ma D, Li Y. Genome-wide identification of long intergenic non-coding RNAs for Ralstonia solanacearum resistance in tomato ( Solanum lycopersicum). FRONTIERS IN PLANT SCIENCE 2022; 13:981281. [PMID: 36186038 PMCID: PMC9523475 DOI: 10.3389/fpls.2022.981281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 05/26/2023]
Abstract
There is growing evidences indicating that long intergenic ncRNAs (lincRNAs) play key roles in plant development and stress responses. To research tomato lincRNA functions during the interaction between tomato and Ralstonia solanacearum, RNA-seq data of tomato plants inoculated with R. solanacearum was analyzed. In this study, 315 possible lincRNAs were identified from RNA-seq data. Then 23 differentially expressed lincRNAs between tomato plants inoculated with R. solanacearum and control were identified and a total of 171 possible target genes for these differentially expressed lincRNAs were predicted. Through GO and KEGG analysis, we found that lincRNA might be involved in jasmonic acid and ethylene signaling pathways to respond to tomato bacterial wilt infection. Furthermore, lincRNA may also be involved in regulating the expression of AGO protein. Subsequently, analysis of expression patterns between differentially expressed lincRNAs and adjacent mRNAs by qRT-PCR revealed that part of lincRNAs and their possible target genes exhibited positive correlation. Taken together, these results suggest that lincRNAs play potential roles in tomato against R. solanacearum infection and will provide fundamental information about the lincRNA-based plant defense mechanisms.
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Affiliation(s)
- Peina Cao
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yan Li
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
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Guo Y, Xu H, Chen B, Grünhofer P, Schreiber L, Lin J, Zhao Y. Genome-wide analysis of long non-coding RNAs in shoot apical meristem and vascular cambium in Populus tomentosa. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153759. [PMID: 35820347 DOI: 10.1016/j.jplph.2022.153759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Shoot apical and lateral meristems play essential roles in the formation and development of primary and secondary growth in plants. A delicate regulatory mechanism is needed to maintain homeostatic balance between the primary and secondary growth, as well as the self-renewal of meristems with the rate of cell division and differentiation of new meristems. However, little is known about the roles of long non-coding RNAs (lncRNAs) in the regulation of maintenance and differentiation of primary and secondary growth in Populus, especially in the cambium division and differentiation into secondary xylem. Here, 1298 lncRNAs were identified both in the apical meristem and vascular cambium, with 80 lncRNAs being expressed only in shoot apical meristem and 45 only in vascular cambium. There are 410 differentially expressed lncRNAs in shoot apical meristem and vascular cambium, among which 271 lncRNAs were up-regulated and 139 were down-regulated in cambium. The GO enrichment analysis revealed that differentially expressed lncRNAs mainly influenced the expression of lncRNAs related to the ribosome pathway, plant hormone signal pathway and photosynthesis pathway. The differentially expressed lncRNAs mainly target mRNA through cis-regulation in the vascular cambium. In addition, six key lncRNAs and also their significantly upregulated target genes were identified. Theses target genes are involved in plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. In addition, six key lncRNAs were identified, their significantly upregulated target genes are related to plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. Investigating lncRNA-mRNA interactions, we further found some genes that may be related to the development of vascular cambium, such as domain-containing transcription factors, cellulose synthesis genes, calcium dependent protein kinase 2, cytokinin receptor 1, glycosyl transferase and polyphenol oxidase. Our findings provide new insights into the lncRNA-mRNA networks in the development of vascular cambium of secondary growth in Populus.
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Affiliation(s)
- Yayu Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Bo Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Paul Grünhofer
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Yuanyuan Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
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Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits.
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Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. Genes (Basel) 2021; 12:genes12091374. [PMID: 34573356 PMCID: PMC8467702 DOI: 10.3390/genes12091374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Adipose is an important body tissue in pigs, and fatty traits are critical in pig production. The function of long non-coding RNA (lncRNA) in fat deposition and metabolism has been found in previous studies. In this study, we collected the adipose tissue of six Landrace pigs with contrast backfat thickness (nhigh = 3, nlow = 3), after which we performed strand-specific RNA sequencing (RNA-seq) based on pooling and biological replicate methods. Biological replicate and pooling RNA-seq revealed 1870 and 1618 lncRNAs, respectively. Using edgeR, we determined that 1512 genes and 220 lncRNAs, 2240 genes and 127 lncRNAs were differentially expressed in biological replicate and pooling RNA-seq, respectively. After target gene prediction, we found that ACSL3 was cis-targeted by lncRNA TCONS-00052400 and could activate the conversion of long-chain fatty acids. In addition, lncRNA TCONS_00041740 cis-regulated gene ACACB regulated the rate-limiting enzyme in fatty acid oxidation. Since these genes have necessary functions in fat metabolism, the results imply that the lncRNAs detected in our study may affect backfat deposition in swine through regulation of their target genes. Our study explored the regulation of lncRNA and their target genes in porcine backfat deposition and provided new insights for further investigation of the biological functions of lncRNA.
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Chen Q, Liu K, Yu R, Zhou B, Huang P, Cao Z, Zhou Y, Wang J. From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:650926. [PMID: 34163498 PMCID: PMC8215657 DOI: 10.3389/fpls.2021.650926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Pingping Huang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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Cao W, Gan L, Wang C, Zhao X, Zhang M, Du J, Zhou S, Zhu C. Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:619062. [PMID: 33643350 PMCID: PMC7902931 DOI: 10.3389/fpls.2021.619062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/06/2021] [Indexed: 05/26/2023]
Abstract
Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato (Solanum tuberosum L.) resistance to Phytophthora infestans (P. infestans) largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of StLNC0004 in Nicotiana benthamiana significantly suppresses P. infestans growth compared with a control, and the expression of extensin (NbEXT), the ortholog of the StLNC0004 target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to P. infestans infection.
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Yan X, Ma L, Yang M. Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas. Sci Rep 2020; 10:10395. [PMID: 32587349 PMCID: PMC7316758 DOI: 10.1038/s41598-020-67410-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in plant development. However, the information of lncRNAs in Jatropha curcas remains largely unexplored. Thus, an attempt has been made in J. curcas to identify 1,850 lncRNAs based on deep sequencing of developing seeds at three typical stages. About ten percent lncRNAs (196 lncRNAs) were differentially expressed lncRNAs during seed developing process. Together with reverse transcription quantitative real-time PCR, the lncRNA expression analyses revealed the stage-specific expression patterns of some novel lncRNAs in J. curcas. The target genes of lncRNAs were annotated for their roles in various biological processes such as gene expression, metabolism, and cell growth. Besides, 10 lncRNAs were identified as the precursors of microRNAs and 26 lncRNAs were predicted to be the targets of Jatropha miRNAs. A total of 31 key lncRNAs play critical roles in the seed developing process in the context of cell growth and development, lipid metabolism, and seed maturation. Our study provides the first systematic study of lncRNAs in the developing seeds of J. curcas and facilitates the functional research of plant lncRNAs and the regulation of seed development.
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Affiliation(s)
- Xihuan Yan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Lanqing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, People's Republic of China. .,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
| | - MingFeng Yang
- Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
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Tiwari JK, Buckseth T, Zinta R, Saraswati A, Singh RK, Rawat S, Chakrabarti SK. Genome-wide identification and characterization of microRNAs by small RNA sequencing for low nitrogen stress in potato. PLoS One 2020; 15:e0233076. [PMID: 32428011 PMCID: PMC7237020 DOI: 10.1371/journal.pone.0233076] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/28/2020] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is an important nutrient for plant growth and tuber quality of potato. Since potato crop requires high dose of N, improving nitrogen use efficiency (NUE) of plant is an inevitable approach to minimize N fertilization. The aim of this study was to identify and characterize microRNAs (miRNAs) by small RNA sequencing in potato plants grown in aeroponic under two contrasting N (high and low) regimes. A total of 119 conserved miRNAs belonging to 41 miRNAs families, and 1002 putative novel miRNAs were identified. From total, 52 and 54 conserved miRNAs, and 404 and 628 putative novel miRNAs were differentially expressed in roots and shoots, respectively under low N stress. Of total 34,135 predicted targets, the gene ontology (GO) analysis indicated that maximum targets belong to biological process followed by molecular function and cellular component. Eexpression levels of the selected miRNAs and targets were validated by real time-quantitative polymerase chain reaction (RT-qPCR) analysis. Two predicted targets of potential miRNAs (miR397 and miR398) were validated by 5' RLM-RACE (RNA ligase mediated rapid amplification of cDNA ends). In general, predicted targets are associated with stress-related, kinase, transporters and transcription factors such as universal stress protein, heat shock protein, salt-tolerance protein, calmodulin binding protein, serine-threonine protein kinsae, Cdk10/11- cyclin dependent kinase, amino acid transporter, nitrate transporter, sugar transporter, transcription factor, F-box family protein, and zinc finger protein etc. Our study highlights that miR397 and miR398 play crucial role in potato during low N stress management. Moreover, study provides insights to modulate miRNAs and their predicted targets to develop N-use efficient potato using transgenic/genome-editing tools in future.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- * E-mail:
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Aastha Saraswati
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Shashi Rawat
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Swarup Kumar Chakrabarti
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Kumar H, Srikanth K, Park W, Lee SH, Choi BH, Kim H, Kim YM, Cho ES, Kim JH, Lee JH, Jung JY, Go GW, Lee KT, Kim JM, Lee J, Lim D, Park JE. Transcriptome analysis to identify long non coding RNA (lncRNA) and characterize their functional role in back fat tissue of pig. Gene 2019; 703:71-82. [PMID: 30954676 DOI: 10.1016/j.gene.2019.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 04/03/2019] [Indexed: 12/12/2022]
Abstract
Long non coding RNAs (lncRNA) have been previously found to be involved in important cellular activities like epigenetics, implantation, cell growth etc. in pigs. However, comprehensive analysis of lncRNA in back fat tissues at different developmental stages in pigs is still lacking. In this study we conducted transcriptome analysis in the back fat tissue of a F1 crossbred Korean Native Pig (KNP) × Yorkshire Pig to identify lncRNA. We investigated their role in 16 pigs at two different growth stages; stage 1 (10 weeks, n = 8) and stage 2 (26 weeks, n = 8). After quality assessment of sequencing reads, we got a total of 1,641,165 assembled transcripts out of eight paired end read from each stage. Among them, 6808 lncRNA transcripts were identified by filtering on the basis of multiple parameters like read length ≥ 200 nucleotides, exon numbers ≥2, FPKM ≥0.5, coding potential score < 0 etc. PFAM and RFAM were used to filter out all possible protein coding genes and housekeeping RNAs respectively. A total of 103 lncRNAs and 1057 mRNAs were found to be differentially expressed (DE) between the two stages (|log2FC| > 2, q < 0.05). We also identified 306 genes located around 100 kb upstream and 234 genes downstream around these DE lncRNA transcripts. The expression of top eleven DE lncRNAs (COL4A6, LY7S, MYH2, OXCT1, SMPDL3A, TMEM182, TTC36, RFOOOO4, RFOOO15, RFOOO45, CADM2) had been validating by qRT-PCR. Pathway and GO terms analysis showed that, positive regulation of biosynthetic process, Wnt signaling pathway, cellular protein modification process, and positive regulation of nitrogen compound were differentially enriched. Our results suggested that, KEGG pathways such as protein digestion and absorption, Arrhythmogenic right ventricular cardiomyopathy (ARVC) to be significantly enriched in both DE lncRNAs as well as DE mRNAs and involved in back fat tissues development. It also suggests that, identified lncRNAs are involved in regulation of important adipose tissues development pathways.
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Affiliation(s)
- Himansu Kumar
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Woncheol Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Seung-Hoon Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Bong-Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Hana Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Yong-Min Kim
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Republic of Korea
| | - Eun-Seok Cho
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Republic of Korea
| | - Jin Hyoung Kim
- Animal Products Research and Development Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea
| | - Jang Hee Lee
- Department of Companion Animal, Seoul Hoseo Occupational Training College, Seoul 07583, Republic of Korea
| | - Ji Yeon Jung
- Department of Food and Nutrition, Hanyang University, Seoul 04763, Republic of Korea
| | - Gwang-Woong Go
- Department of Food and Nutrition, Hanyang University, Seoul 04763, Republic of Korea
| | - Kyung-Tai Lee
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Cheonan 31000, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Jungjae Lee
- Jung P& C Institute, Inc., 1504 U-Tower, Yongin-si, Gyeonggi-do 16950, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea.
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13
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Yan N, Du Y, Zhang H, Zhang Z, Liu X, Shi J, Liu Y. RNA Sequencing Provides Insights into the Regulation of Solanesol Biosynthesis in Nicotiana tabacum Induced by Moderately High Temperature. Biomolecules 2018; 8:E165. [PMID: 30544626 PMCID: PMC6316125 DOI: 10.3390/biom8040165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/02/2018] [Accepted: 12/02/2018] [Indexed: 12/19/2022] Open
Abstract
Solanesol is a terpene alcohol composed of nine isoprene units that mainly accumulates in solanaceous plants, especially tobacco (Nicotiana tabacum). The present study aimed to investigate the regulation of solanesol accumulation in tobacco leaves induced by moderately high temperature (MHT). Exposure to MHT resulted in a significant increase in solanesol content, dry weight, and net photosynthetic rate in tobacco leaves. In MHT-exposed tobacco leaves, 492 and 1440 genes were significantly up- and downregulated, respectively, as revealed by RNA-sequencing. Functional enrichment analysis revealed that most of the differentially expressed genes (DEGs) were mainly related to secondary metabolite biosynthesis, metabolic pathway, carbohydrate metabolism, lipid metabolism, hydrolase activity, catalytic activity, and oxidation-reduction process. Moreover, 122 transcription factors of DEGs were divided into 22 families. Significant upregulation of N. tabacum 3-hydroxy-3-methylglutaryl-CoA reductase (NtHMGR), 1-deoxy-d-xylulose 5-phosphate reductoisomerase (NtDXR), geranylgeranyl diphosphate synthase (NtGGPS), and solanesyl diphosphate synthase (NtSPS) and significant downregulation of N. tabacum 1-deoxy-d-xylulose 5-phosphate synthase (NtDXS) and farnesyl diphosphate synthase (NtFPS) transcription upon MHT exposure were monitored by quantitative real-time PCR (qRT-PCR). This study indicated that solanesol accumulation in tobacco leaves can be manipulated through regulation of the environmental temperature and established a basis for further elucidation of the molecular mechanism of temperature regulation of solanesol accumulation.
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Affiliation(s)
- Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Yongmei Du
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Hongbo Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Zhongfeng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Xinmin Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - John Shi
- Guelph Food Research Center, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada.
| | - Yanhua Liu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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14
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Li WQ, Jia YL, Liu FQ, Wang FQ, Fan FJ, Wang J, Zhu JY, Xu Y, Zhong WG, Yang J. Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice. RSC Adv 2018; 8:34408-34417. [PMID: 35548658 PMCID: PMC9087051 DOI: 10.1039/c8ra04993a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/09/2018] [Indexed: 11/26/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4709 lncRNAs identified, 2518 and 2191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of five lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.
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Affiliation(s)
- Wen Qi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Yu Lin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center Stuttgart 72160 USA
| | - Feng Quan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Fang Quan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Fang Jun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jin Yan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Wei Gong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
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