Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)
Abstract Background Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. Results In this study, two peanut recombinant inbred lines (R...
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-020-02405-4 |
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| author | Xingli Ma Xingguo Zhang Sy Mamadou Traore Zeyu Xin Longlong Ning Ke Li Kunkun Zhao Zhongfeng Li Guohao He Dongmei Yin |
| author_facet | Xingli Ma Xingguo Zhang Sy Mamadou Traore Zeyu Xin Longlong Ning Ke Li Kunkun Zhao Zhongfeng Li Guohao He Dongmei Yin |
| author_sort | Xingli Ma |
| collection | DOAJ |
| description | Abstract Background Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. Results In this study, two peanut recombinant inbred lines (RIL8) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development. Conclusions These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development. |
| first_indexed | 2024-12-10T06:38:32Z |
| format | Article |
| id | doaj.art-23f3cba5d86a486ab9ca624bbd186918 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-10T06:38:32Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-23f3cba5d86a486ab9ca624bbd1869182022-12-22T01:58:50ZengBMCBMC Plant Biology1471-22292020-05-0120111410.1186/s12870-020-02405-4Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.)Xingli Ma0Xingguo Zhang1Sy Mamadou Traore2Zeyu Xin3Longlong Ning4Ke Li5Kunkun Zhao6Zhongfeng Li7Guohao He8Dongmei Yin9College of Agronomy, Henan Agricultural UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agriculture, Environment and Nutrition Sciences, Tuskegee UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agronomy, Henan Agricultural UniversityCollege of Agriculture, Environment and Nutrition Sciences, Tuskegee UniversityCollege of Agronomy, Henan Agricultural UniversityAbstract Background Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. Results In this study, two peanut recombinant inbred lines (RIL8) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development. Conclusions These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development.http://link.springer.com/article/10.1186/s12870-020-02405-4PeanutlncRNASeed developmentRNA-SeqTranscriptional regulation |
| spellingShingle | Xingli Ma Xingguo Zhang Sy Mamadou Traore Zeyu Xin Longlong Ning Ke Li Kunkun Zhao Zhongfeng Li Guohao He Dongmei Yin Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) BMC Plant Biology Peanut lncRNA Seed development RNA-Seq Transcriptional regulation |
| title | Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) |
| title_full | Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) |
| title_fullStr | Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) |
| title_full_unstemmed | Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) |
| title_short | Genome-wide identification and analysis of long noncoding RNAs (lncRNAs) during seed development in peanut (Arachis hypogaea L.) |
| title_sort | genome wide identification and analysis of long noncoding rnas lncrnas during seed development in peanut arachis hypogaea l |
| topic | Peanut lncRNA Seed development RNA-Seq Transcriptional regulation |
| url | http://link.springer.com/article/10.1186/s12870-020-02405-4 |
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