Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa
Abstract Background Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental facto...
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-04031-8 |
| _version_ | 1828069628352397312 |
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| author | Aboozar Soorni Marzieh Karimi Batoul Al Sharif Khashayar Habibi |
| author_facet | Aboozar Soorni Marzieh Karimi Batoul Al Sharif Khashayar Habibi |
| author_sort | Aboozar Soorni |
| collection | DOAJ |
| description | Abstract Background Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. Results For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. Conclusion Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study. |
| first_indexed | 2024-04-11T00:23:58Z |
| format | Article |
| id | doaj.art-63966d1348ac4175aec8f3393cdc9b70 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-11T00:23:58Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-63966d1348ac4175aec8f3393cdc9b702023-01-08T12:08:28ZengBMCBMC Plant Biology1471-22292023-01-0123111910.1186/s12870-022-04031-8Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativaAboozar Soorni0Marzieh Karimi1Batoul Al Sharif2Khashayar Habibi3ZarinshahrDepartment of Biotechnology, College of Agriculture, Isfahan University of TechnologyDepartment of Biotechnology, College of Agriculture, Isfahan University of TechnologyDepartment of Biotechnology, College of Agriculture, Isfahan University of TechnologyAbstract Background Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. Results For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. Conclusion Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.https://doi.org/10.1186/s12870-022-04031-8BoltingLong non-coding RNALettuceRegulation |
| spellingShingle | Aboozar Soorni Marzieh Karimi Batoul Al Sharif Khashayar Habibi Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa BMC Plant Biology Bolting Long non-coding RNA Lettuce Regulation |
| title | Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa |
| title_full | Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa |
| title_fullStr | Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa |
| title_full_unstemmed | Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa |
| title_short | Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa |
| title_sort | genome wide screening and characterization of long noncoding rnas involved in flowering bolting of lactuca sativa |
| topic | Bolting Long non-coding RNA Lettuce Regulation |
| url | https://doi.org/10.1186/s12870-022-04031-8 |
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