Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves
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 cin...
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BMC
2025-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-11171-8 |
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| author | Haojie Shi Guijuan Ding Yun Wang Jiaqi Wang Xiaoli Wang Dan Wang Ping Lu |
| author_facet | Haojie Shi Guijuan Ding Yun Wang Jiaqi Wang Xiaoli Wang Dan Wang Ping Lu |
| author_sort | Haojie Shi |
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| description | 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. |
| format | Article |
| id | doaj-art-6d22adf3228e4d61a3446d2489087c69 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-6d22adf3228e4d61a3446d2489087c692025-01-12T12:09:15ZengBMCBMC Genomics1471-21642025-01-0126111310.1186/s12864-024-11171-8Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leavesHaojie Shi0Guijuan Ding1Yun Wang2Jiaqi Wang3Xiaoli Wang4Dan Wang5Ping Lu6The 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 UniversityThe 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 UniversityThe 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 UniversityThe 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 UniversityJiangsu Provincial Key Construction Laboratory of Probiotics Preparation, College of Life Science and Food Engineering, Huaiyin Institute of TechnologyState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A & F UniversityThe 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 UniversityAbstract 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.https://doi.org/10.1186/s12864-024-11171-8Botrytis cinereaTranscriptomeLong noncoding RNAsSolanum lycopersicumAlternative splicing |
| spellingShingle | Haojie Shi Guijuan Ding Yun Wang Jiaqi Wang Xiaoli Wang Dan Wang Ping Lu Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves BMC Genomics Botrytis cinerea Transcriptome Long noncoding RNAs Solanum lycopersicum Alternative splicing |
| title | Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves |
| title_full | Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves |
| title_fullStr | Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves |
| title_full_unstemmed | Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves |
| title_short | Genome-wide identification of long non-coding RNA for Botrytis cinerea during infection to tomato (Solanum lycopersicum) leaves |
| title_sort | genome wide identification of long non coding rna for botrytis cinerea during infection to tomato solanum lycopersicum leaves |
| topic | Botrytis cinerea Transcriptome Long noncoding RNAs Solanum lycopersicum Alternative splicing |
| url | https://doi.org/10.1186/s12864-024-11171-8 |
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