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Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development
BACKGROUND: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regula...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335773/ https://www.ncbi.nlm.nih.gov/pubmed/28253861 http://dx.doi.org/10.1186/s12864-017-3587-8 |
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author | Gao, Chao Wang, Pengfei Zhao, Shuzhen Zhao, Chuanzhi Xia, Han Hou, Lei Ju, Zheng Zhang, Ye Li, Changsheng Wang, Xingjun |
author_facet | Gao, Chao Wang, Pengfei Zhao, Shuzhen Zhao, Chuanzhi Xia, Han Hou, Lei Ju, Zheng Zhang, Ye Li, Changsheng Wang, Xingjun |
author_sort | Gao, Chao |
collection | PubMed |
description | BACKGROUND: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored. RESULTS: In this study, small RNA and degradome libraries from peanut early pod of different developmental stages were constructed and sequenced. A total of 70 known and 24 novel miRNA families were discovered. Among them, 16 miRNA families were legume-specific and 12 families were peanut-specific. 30 known and 10 novel miRNA families were differentially expressed during pod development. In addition, 115 target genes were identified for 47 miRNA families by degradome sequencing. Several new targets that might be specific to peanut were found and further validated by RNA ligase-mediated rapid amplification of 5′ cDNA ends (RLM 5′-RACE). Furthermore, we performed profiling analysis of intact and total transcripts of several target genes, demonstrating that SPL (miR156/157), NAC (miR164), PPRP (miR167 and miR1088), AP2 (miR172) and GRF (miR396) are actively modulated during early pod development, respectively. CONCLUSIONS: Large numbers of miRNAs and their related target genes were identified through deep sequencing. These findings provided new information on miRNA-mediated regulatory pathways in peanut pod, which will contribute to the comprehensive understanding of the molecular mechanisms that governing peanut embryo and early pod development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3587-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5335773 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53357732017-03-07 Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development Gao, Chao Wang, Pengfei Zhao, Shuzhen Zhao, Chuanzhi Xia, Han Hou, Lei Ju, Zheng Zhang, Ye Li, Changsheng Wang, Xingjun BMC Genomics Research Article BACKGROUND: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored. RESULTS: In this study, small RNA and degradome libraries from peanut early pod of different developmental stages were constructed and sequenced. A total of 70 known and 24 novel miRNA families were discovered. Among them, 16 miRNA families were legume-specific and 12 families were peanut-specific. 30 known and 10 novel miRNA families were differentially expressed during pod development. In addition, 115 target genes were identified for 47 miRNA families by degradome sequencing. Several new targets that might be specific to peanut were found and further validated by RNA ligase-mediated rapid amplification of 5′ cDNA ends (RLM 5′-RACE). Furthermore, we performed profiling analysis of intact and total transcripts of several target genes, demonstrating that SPL (miR156/157), NAC (miR164), PPRP (miR167 and miR1088), AP2 (miR172) and GRF (miR396) are actively modulated during early pod development, respectively. CONCLUSIONS: Large numbers of miRNAs and their related target genes were identified through deep sequencing. These findings provided new information on miRNA-mediated regulatory pathways in peanut pod, which will contribute to the comprehensive understanding of the molecular mechanisms that governing peanut embryo and early pod development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3587-8) contains supplementary material, which is available to authorized users. BioMed Central 2017-03-02 /pmc/articles/PMC5335773/ /pubmed/28253861 http://dx.doi.org/10.1186/s12864-017-3587-8 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Gao, Chao Wang, Pengfei Zhao, Shuzhen Zhao, Chuanzhi Xia, Han Hou, Lei Ju, Zheng Zhang, Ye Li, Changsheng Wang, Xingjun Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title | Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title_full | Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title_fullStr | Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title_full_unstemmed | Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title_short | Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development |
title_sort | small rna profiling and degradome analysis reveal regulation of microrna in peanut embryogenesis and early pod development |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335773/ https://www.ncbi.nlm.nih.gov/pubmed/28253861 http://dx.doi.org/10.1186/s12864-017-3587-8 |
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