1
|
Shi H, Ding G, Wang Y, Wang J, Wang X, Wang D, Lu P. Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves. BMC Genomics 2025; 26:7. [PMID: 39762752 PMCID: PMC11702200 DOI: 10.1186/s12864-024-11171-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025] Open
Abstract
Long non-coding RNA (lncRNA) plays important roles in animals and plants. In filamentous fungi, however, their biological function in infection stage has been poorly studied. Here, we investigated the landscape and regulation of lncRNA in the filamentous plant pathogenic fungus Botrytis cinerea by strand-specific RNA-seq of multiple infection stages. In total, 1837 lncRNAs have been identified in B. cinerea. A large number of lncRNAs were found to be antisense to mRNAs, forming 743 sense-antisense pairs, of which 55 antisense lncRNAs and their respective sense transcripts were induced in parallel as the infection stage. Although small RNAs were produced from these overlapping loci, antisense lncRNAs appeared not to be involved in gene silencing pathways. In addition, we found the alternative splicing events occurred in lncRNA. These results highlight the developmental stage-specific nature and functional potential of lncRNA expression in the infection stage and provide fundamental resources for studying infection stage-induced lncRNAs.
Collapse
Affiliation(s)
- Haojie Shi
- The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Guijuan Ding
- The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yun Wang
- The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiaqi Wang
- The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xiaoli Wang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Dan Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Ping Lu
- The Key Lab for Biology of Crop Pathogens and Insect Pests and Their Ecological Regulation of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China.
| |
Collapse
|
2
|
Xu J, Shen E, Guo F, Wang K, Hu Y, Shen L, Chen H, Li X, Zhu QH, Fan L, Chu Q. Identification of cell-type specificity, trans- and cis-acting functions of plant lincRNAs from single-cell transcriptomes. THE NEW PHYTOLOGIST 2025; 245:698-710. [PMID: 39550625 DOI: 10.1111/nph.20269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Accepted: 10/21/2024] [Indexed: 11/18/2024]
Abstract
Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single-cell RNA sequencing (scRNA-seq) technology has opened up a valuable avenue for scrutinizing the intricate roles of lincRNAs in cellular processes. Here, we identified a new batch of lincRNAs using scRNA-seq data from diverse tissues of plants (rice, Arabidopsis, tomato, and maize). Based on well-annotated single-cell transcriptome atlases, plant lincRNAs were found to possess the same level of cell-type specificity as mRNAs and to be involved in the differentiation of certain cell types based on pseudo-time analysis. Many lincRNAs were predicted to play a hub role in the cell-type-specific co-expression networks of lincRNAs and mRNAs, suggesting their trans-acting abilities. Besides, plant lincRNAs were revealed to have potential cis-acting properties based on their genomic distances and expression correlations with the neighboring mRNAs. Furthermore, an online platform, PscLncRNA (http://ibi.zju.edu.cn/psclncrna/), was constructed for searching and visualizing all identified plant lincRNAs with annotated potential functions. Our work provides new insights into plant lincRNAs at single-cell resolution and an important resource for understanding and further investigation of plant lincRNAs.
Collapse
Affiliation(s)
- Jiwei Xu
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Fu Guo
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Kaiqiang Wang
- Hainan Institute, Zhejiang University, Sanya, 572025, China
| | - Yurong Hu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Leti Shen
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Hongyu Chen
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohan Li
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Longjiang Fan
- Hainan Institute, Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qinjie Chu
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| |
Collapse
|
3
|
Liao L, Zhao Z, Zhang R, Luo C, Hu Y, Yu Z, Cui J. Correlation Between Effector Gene Expression Targeted by lncRNAs in the Oomycete Fish Pathogen, Saprolegnia parasitica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 27:3. [PMID: 39576381 DOI: 10.1007/s10126-024-10385-x] [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: 08/23/2024] [Accepted: 10/09/2024] [Indexed: 11/24/2024]
Abstract
Saprolegniasis caused by Saprolegnia parasitica leads to significant economic losses in the aquaculture industry worldwide. Effector proteins secreted by pathogens are key molecules involved in their pathogenicity and long non-coding lncRNAs (lncRNAs) act as regulators in these processes. However, little is known about the lncRNAs and effector proteins in S. parasitica. Here, we first identified 1027 lncRNAs during the developmental stages and infection process of S. parasitica. Compared with mRNAs, these lncRNAs had shorter sequences and exon lengths and lower expression levels. In addition, their sequence conservation among other oomycete species was also low. The S. parasitica lncRNAs were characterized according to developmental stage and infection time point. We also identified effector proteins using a computational pipeline. In total, 131 S. parasitica effector proteins were identified and classified into 34 families. The 47 genes encoding effector genes were neighbors of 39 lncRNAs, and there was a correlation between the transcription level of lncRNAs and their neighboring genes. Gain- and loss-of-function experiments revealed that lncRNA8375.2 promoted the expression of a neighboring effector gene, SpCAP. Our results provide new data on S. parasitica lncRNAs and effector proteins, and provide insights into the lncRNA-effector module involved in S. parasitica.
Collapse
Affiliation(s)
- Lijuan Liao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Zihao Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Ruoxiao Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Chaoqun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Yibo Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziquan Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Jun Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China.
| |
Collapse
|
4
|
Liu Q, Xue J, Zhang L, Jiang L, Li C. Unveiling the Roles of LncRNA MOIRAs in Rice Blast Disease Resistance. Genes (Basel) 2024; 15:82. [PMID: 38254971 PMCID: PMC10815219 DOI: 10.3390/genes15010082] [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: 11/07/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is a major threat to rice production worldwide. This study investigates the role of long non-coding RNAs (lncRNAs) in rice's response to this destructive disease, with a focus on their impacts on disease resistance and yield traits. Three specific lncRNAs coded by M. oryzae infection-responsive lncRNAs (MOIRAs), MOIRA1, MOIRA2, and MOIRA3, were identified as key regulators of rice's response to M. oryzae infection. Strikingly, when MOIRA1 and MOIRA2 were overexpressed, they exhibited a dual function: they increased rice's susceptibility to blast fungus, indicating a negative role in disease resistance, while simultaneously enhancing tiller numbers and single-plant yield, with no adverse effects on other yield-related traits. This unexpected improvement in productivity suggests the possibility of overcoming the traditional trade-off between disease resistance and crop yield. These findings provide a novel perspective on crop enhancement, offering a promising solution to global food security challenges by developing rice varieties that effectively balance disease resistance and increased productivity.
Collapse
Affiliation(s)
- Qing Liu
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Jiao Xue
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Lanlan Zhang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Liqun Jiang
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| | - Chen Li
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (L.Z.); (L.J.); (C.L.)
| |
Collapse
|
5
|
Qian J, Ibrahim HMM, Erz M, Kümmel F, Panstruga R, Kusch S. Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen. Mob DNA 2023; 14:17. [PMID: 37964319 PMCID: PMC10648671 DOI: 10.1186/s13100-023-00305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/18/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle. RESULTS We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes. CONCLUSIONS Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.
Collapse
Affiliation(s)
- Jiangzhao Qian
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Heba M M Ibrahim
- Department of Biosystems, Division of Plant Biotechnics, Faculty of Bioscience Engineering, Katholieke Universiteit Leuven, 3001, Leuven, Belgium
- Present address: Institute of Bio- and Geosciences IBG-2, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Myriam Erz
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
- Present address: Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-Von-Linné-Weg 10, 50829, Cologne, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
- Present address: Institute of Bio- and Geosciences IBG-4, Forschungszentrum Jülich, 52425, Jülich, Germany.
| |
Collapse
|
6
|
Glad HM, Tralamazza SM, Croll D. The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2023; 9. [PMID: 37991492 DOI: 10.1099/mgen.0.001136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.
Collapse
Affiliation(s)
- Hanna M Glad
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| |
Collapse
|
7
|
Liu K, Ma X, Zhao L, Lai X, Chen J, Lang X, Han Q, Wan X, Li C. Comprehensive transcriptomic analysis of three varieties with different brown planthopper-resistance identifies leaf sheath lncRNAs in rice. BMC PLANT BIOLOGY 2023; 23:367. [PMID: 37480003 PMCID: PMC10362764 DOI: 10.1186/s12870-023-04374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been brought great attention for their crucial roles in diverse biological processes. However, systematic identification of lncRNAs associated with specialized rice pest, brown planthopper (BPH), defense in rice remains unexplored. RESULTS In this study, a genome-wide high throughput sequencing analysis was performed using leaf sheaths of susceptible rice Taichung Native 1 (TN1) and resistant rice IR36 and R476 with and without BPH feeding. A total of 2283 lncRNAs were identified, of which 649 lncRNAs were differentially expressed. During BPH infestation, 84 (120 in total), 52 (70 in total) and 63 (94 in total) of differentially expressed lncRNAs were found only in TN1, IR36 and R476, respectively. Through analyzing their cis-, trans-, and target mimic-activities, not only the lncRNAs targeting resistance genes (NBS-LRR and RLKs) and transcription factors, but also the lncRNAs acting as the targets of the well-studied stress-related miRNAs (miR2118, miR528, and miR1320) in each variety were identified. Before the BPH feeding, 238 and 312 lncRNAs were found to be differentially expressed in TN1 vs. IR36 and TN1 vs. R476, respectively. Among their putative targets, the plant-pathogen interaction pathway was significantly enriched. It is speculated that the resistant rice was in a priming state by the regulation of lncRNAs. Furthermore, the lncRNAs extensively involved in response to BPH feeding were identified by Weighted Gene Co-expression Network Analysis (WGCNA), and the possible regulation networks of the key lncRNAs were constructed. These lncRNAs regulate different pathways that contribute to the basal defense and specific resistance of rice to the BPH. CONCLUSION In summary, we identified the specific lncRNAs targeting the well-studied stress-related miRNAs, resistance genes, and transcription factors in each variety during BPH infestation. Additionally, the possible regulating network of the lncRNAs extensively responding to BPH feeding revealed by WGCNA were constructed. These findings will provide further understanding of the regulatory roles of lncRNAs in BPH defense, and lay a foundation for functional research on the candidate lncRNAs.
Collapse
Affiliation(s)
- Kai Liu
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaozhi Ma
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510642, China
| | - Luyao Zhao
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaofeng Lai
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jie Chen
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xingxuan Lang
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Qunxin Han
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xiaorong Wan
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Chunmei Li
- Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests & Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| |
Collapse
|
8
|
Yi K, Yan W, Li X, Yang S, Li J, Yin Y, Yuan F, Wang H, Kang Z, Han D, Zeng Q. Identification of Long Intergenic Noncoding RNAs in Rhizoctonia cerealis following Inoculation of Wheat. Microbiol Spectr 2023; 11:e0344922. [PMID: 37036374 PMCID: PMC10269763 DOI: 10.1128/spectrum.03449-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/12/2023] [Indexed: 04/11/2023] Open
Abstract
Wheat sharp eyespot caused by Rhizoctonia cerealis is primarily a severe threat to worldwide wheat production. Currently, there are no resistant wheat cultivars, and the use of fungicides is the primary method for controlling this disease. Elucidating the mechanisms of R. cerealis pathogenicity can accelerate the pace of the control of this disease. Long intergenic noncoding RNAs (lincRNAs) that function in plant-pathogen interactions might provide a new perspective. We systematically analyzed lincRNAs and identified a total of 1,319 lincRNAs in R. cerealis. We found that lincRNAs are involved in various biological processes, as shown by differential expression analysis and weighted correlation network analysis (WGCNA). Next, one of nine hub lincRNAs in the blue module that was related to infection and growth processes, MSTRG.4380.1, was verified to reduce R. cerealis virulence on wheat by a host-induced gene silencing (HIGS) assay. Following that, RNA sequencing (RNA-Seq) analysis revealed that the significantly downregulated genes in the MSTRG.4380.1 knockdown lines were associated mainly with infection-related processes, including hydrolase, transmembrane transporter, and energy metabolism activities. Additionally, 23 novel microRNAs (miRNAs) were discovered during small RNA (sRNA) sequencing (sRNA-Seq) analysis of MSTRG.4380.1 knockdown, and target prediction of miRNAs suggested that MSTRG.4380.1 does not act as a competitive endogenous RNA (ceRNA). This study performed the first genome-wide identification of R. cerealis lincRNAs and miRNAs. It confirmed the involvement of a lincRNA in the infection process, providing new insights into the mechanism of R. cerealis infection and offering a new approach for protecting wheat from R. cerealis. IMPORTANCE Rhizoctonia cerealis, the primary causal agent of wheat sharp eyespot, has caused significant losses in worldwide wheat production. Since no resistant wheat cultivars exist, chemical control is the primary method. However, this approach is environmentally unfriendly and costly. RNA interference (RNAi)-mediated pathogenicity gene silencing has been proven to reduce the growth of Rhizoctonia and provides a new perspective for disease control. Recent studies have shown that lincRNAs are involved in various biological processes across species, such as biotic and abiotic stresses. Therefore, verifying the function of lincRNAs in R. cerealis is beneficial for understanding the infection mechanism. In this study, we reveal that lincRNAs could contribute to the virulence of R. cerealis, which provides new insights into controlling this pathogen.
Collapse
Affiliation(s)
- Ke Yi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Weiyi Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuqing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiaqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Yifan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|