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Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.).
PLoS One. 2013; 8(7):e69995.Plos

Abstract

BACKGROUND

MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean.

RESULTS

Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed.

CONCLUSIONS

The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae.

Authors+Show Affiliations

Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23894571

Citation

Xu, Wei, et al. "Transcriptome-wide Identification and Characterization of microRNAs From Castor Bean (Ricinus Communis L.)." PloS One, vol. 8, no. 7, 2013, pp. e69995.
Xu W, Cui Q, Li F, et al. Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.). PLoS One. 2013;8(7):e69995.
Xu, W., Cui, Q., Li, F., & Liu, A. (2013). Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.). PloS One, 8(7), e69995. https://doi.org/10.1371/journal.pone.0069995
Xu W, et al. Transcriptome-wide Identification and Characterization of microRNAs From Castor Bean (Ricinus Communis L.). PLoS One. 2013;8(7):e69995. PubMed PMID: 23894571.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.). AU - Xu,Wei, AU - Cui,Qinghua, AU - Li,Fei, AU - Liu,Aizhong, Y1 - 2013/07/24/ PY - 2013/03/28/received PY - 2013/06/14/accepted PY - 2013/7/30/entrez PY - 2013/7/31/pubmed PY - 2014/2/22/medline SP - e69995 EP - e69995 JF - PloS one JO - PLoS One VL - 8 IS - 7 N2 - BACKGROUND: MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean. RESULTS: Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed. CONCLUSIONS: The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/23894571/Transcriptome_wide_identification_and_characterization_of_microRNAs_from_castor_bean__Ricinus_communis_L___ L2 - https://dx.plos.org/10.1371/journal.pone.0069995 DB - PRIME DP - Unbound Medicine ER -