Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i>
Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid <i>Cucumis hytivus</i>...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/12/1500 |
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| author | Panqiao Wang Xiaqing Yu Zaobing Zhu Yufei Zhai Qinzheng Zhao Ya Meng Ji Li Qunfeng Lou Jinfeng Chen |
| author_facet | Panqiao Wang Xiaqing Yu Zaobing Zhu Yufei Zhai Qinzheng Zhao Ya Meng Ji Li Qunfeng Lou Jinfeng Chen |
| author_sort | Panqiao Wang |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid <i>Cucumis hytivus</i> (S<sub>14</sub>), its diploid parents, and the F<sub>1</sub> hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in <i>C. hytivus</i>, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S<sub>14</sub>, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution. |
| first_indexed | 2024-03-10T14:06:53Z |
| format | Article |
| id | doaj.art-6b5e09e089b54339b6b0ed3d515212fd |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T14:06:53Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-6b5e09e089b54339b6b0ed3d515212fd2023-11-21T00:33:54ZengMDPI AGGenes2073-44252020-12-011112150010.3390/genes11121500Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i>Panqiao Wang0Xiaqing Yu1Zaobing Zhu2Yufei Zhai3Qinzheng Zhao4Ya Meng5Ji Li6Qunfeng Lou7Jinfeng Chen8State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaState Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, ChinaLong non-coding RNAs (lncRNAs) play critical regulatory roles in various biological processes. However, the presence of lncRNAs and how they function in plant polyploidy are still largely unknown. Hence, we examined the profile of lncRNAs in a nascent allotetraploid <i>Cucumis hytivus</i> (S<sub>14</sub>), its diploid parents, and the F<sub>1</sub> hybrid, to reveal the function of lncRNAs in plant-interspecific hybridization and whole genome duplication. Results showed that 2206 lncRNAs evenly transcribed from all 19 chromosomes were identified in <i>C. hytivus</i>, 44.6% of which were from intergenic regions. Based on the expression trend in allopolyploidization, we found that a high proportion of lncRNAs (94.6%) showed up-regulated expression to varying degrees following hybridization. However, few lncRNAs (33, 2.1%) were non-additively expressed after genome duplication, suggesting the significant effect of hybridization on lncRNAs, rather than genome duplication. Furthermore, 253 cis-regulated target genes were predicted for these differentially expressed lncRNAs in S<sub>14</sub>, which mainly participated in chloroplast biological regulation (e.g., chlorophyll synthesis and light harvesting system). Overall, this study provides new insight into the function of lncRNAs during the processes of hybridization and polyploidization in plant evolution.https://www.mdpi.com/2073-4425/11/12/1500lncRNAsallopolyploid<i>Cucumis</i>transcriptomeinterspecific hybridization |
| spellingShingle | Panqiao Wang Xiaqing Yu Zaobing Zhu Yufei Zhai Qinzheng Zhao Ya Meng Ji Li Qunfeng Lou Jinfeng Chen Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> Genes lncRNAs allopolyploid <i>Cucumis</i> transcriptome interspecific hybridization |
| title | Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> |
| title_full | Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> |
| title_fullStr | Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> |
| title_full_unstemmed | Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> |
| title_short | Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in <i>Cucumis</i> |
| title_sort | global profiling of lncrnas expression responsive to allopolyploidization in i cucumis i |
| topic | lncRNAs allopolyploid <i>Cucumis</i> transcriptome interspecific hybridization |
| url | https://www.mdpi.com/2073-4425/11/12/1500 |
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