Advanced search
1 file | 1.47 MB Add to list

Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos

Author
Organization
Abstract
Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
Keywords
Multidisciplinary

Downloads

  • Rodrigues et al. 2019 Scientific Reports 9 11327.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 1.47 MB

Citation

Please use this url to cite or link to this publication:

MLA
Rodrigues, Andreia S. et al. “Small RNA Profiling in Pinus Pinaster Reveals the Transcriptome of Developing Seeds and Highlights Differences Between Zygotic and Somatic Embryos.” SCIENTIFIC REPORTS 9 (2019): n. pag. Print.
APA
Rodrigues, A. S., Chaves, I., Costa, B. V., Lin, Y.-C., Lopes, S., Milhinhos, A., Van de Peer, Y., et al. (2019). Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. SCIENTIFIC REPORTS, 9.
Chicago author-date
Rodrigues, Andreia S., Inês Chaves, Bruno Vasques Costa, Yao-Cheng Lin, Susana Lopes, Ana Milhinhos, Yves Van de Peer, and Célia M. Miguel. 2019. “Small RNA Profiling in Pinus Pinaster Reveals the Transcriptome of Developing Seeds and Highlights Differences Between Zygotic and Somatic Embryos.” Scientific Reports 9.
Chicago author-date (all authors)
Rodrigues, Andreia S., Inês Chaves, Bruno Vasques Costa, Yao-Cheng Lin, Susana Lopes, Ana Milhinhos, Yves Van de Peer, and Célia M. Miguel. 2019. “Small RNA Profiling in Pinus Pinaster Reveals the Transcriptome of Developing Seeds and Highlights Differences Between Zygotic and Somatic Embryos.” Scientific Reports 9.
Vancouver
1.
Rodrigues AS, Chaves I, Costa BV, Lin Y-C, Lopes S, Milhinhos A, et al. Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. SCIENTIFIC REPORTS. 2019;9.
IEEE
[1]
A. S. Rodrigues et al., “Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos,” SCIENTIFIC REPORTS, vol. 9, 2019.
@article{8624448,
  abstract     = {Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.},
  articleno    = {11327},
  author       = {Rodrigues, Andreia S. and Chaves, Inês and Costa, Bruno Vasques and Lin, Yao-Cheng and Lopes, Susana and Milhinhos, Ana and Van de Peer, Yves and Miguel, Célia M.},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keywords     = {Multidisciplinary},
  language     = {eng},
  title        = {Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos},
  url          = {http://dx.doi.org/10.1038/s41598-019-47789-y},
  volume       = {9},
  year         = {2019},
}

Altmetric
View in Altmetric
Web of Science
Times cited: