Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice
Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:22 |
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| Enthalten in: |
International journal of molecular sciences - 22(2021), 9 vom: 29. Apr. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
He, Huang [VerfasserIn] |
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| Links: |
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| Themen: |
Agronomic traits |
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| Anmerkungen: |
Date Completed 28.05.2021 Date Revised 28.05.2021 published: Electronic Citation Status MEDLINE |
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| doi: |
10.3390/ijms22094742 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM325000190 |
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| 100 | 1 | |a He, Huang |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice |
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| 500 | |a Date Completed 28.05.2021 | ||
| 500 | |a Date Revised 28.05.2021 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Crop domestication, which gives rise to a number of desirable agronomic traits, represents a typical model system of plant evolution. Numerous genomic evidence has proven that noncoding RNAs such as microRNAs and phasiRNAs, as well as protein-coding genes, are selected during crop domestication. However, limited data shows plant long noncoding RNAs (lncRNAs) are also involved in this biological process. In this study, we performed strand-specific RNA sequencing of cultivated rice Oryza sativa ssp. japonica and O. sativa ssp. indica, and their wild progenitor O. rufipogon. We identified a total of 8528 lncRNAs, including 4072 lncRNAs in O. rufipogon, 2091 lncRNAs in japonica rice, and 2365 lncRNAs in indica rice. The lncRNAs expressed in wild rice were revealed to be shorter in length and had fewer exon numbers when compared with lncRNAs from cultivated rice. We also identified a number of conserved lncRNAs in the wild and cultivated rice. The functional study demonstrated that several of these conserved lncRNAs are associated with domestication-related traits in rice. Our findings revealed the feature and conservation of lncRNAs during rice domestication and will further promote functional studies of lncRNAs in rice | ||
| 650 | 4 | |a Comparative Study | |
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a agronomic traits | |
| 650 | 4 | |a conservation | |
| 650 | 4 | |a crop domestication | |
| 650 | 4 | |a cultivated rice | |
| 650 | 4 | |a lncRNAs | |
| 650 | 4 | |a wild rice | |
| 650 | 7 | |a RNA, Long Noncoding |2 NLM | |
| 650 | 7 | |a RNA, Plant |2 NLM | |
| 700 | 1 | |a Zhou, Yan-Fei |e verfasserin |4 aut | |
| 700 | 1 | |a Yang, Yu-Wei |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Zhi |e verfasserin |4 aut | |
| 700 | 1 | |a Lei, Meng-Qi |e verfasserin |4 aut | |
| 700 | 1 | |a Feng, Yan-Zhao |e verfasserin |4 aut | |
| 700 | 1 | |a Zhang, Yu-Chan |e verfasserin |4 aut | |
| 700 | 1 | |a Chen, Yue-Qin |e verfasserin |4 aut | |
| 700 | 1 | |a Lian, Jian-Ping |e verfasserin |4 aut | |
| 700 | 1 | |a Yu, Yang |e verfasserin |4 aut | |
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| 773 | 1 | 8 | |g volume:22 |g year:2021 |g number:9 |g day:29 |g month:04 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.3390/ijms22094742 |3 Volltext |
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