Abstract
Transcript and proteomics studies in embryogenic cultures from Araucaria angustifolia, an endangered native Brazilian conifer with ecological and economic importance, have indicated a role for post-transcriptional regulation in this process. Here, we profiled the miRNA expression pattern using small RNA sequencing technology in two embryogenic cell lines, Responsive- and Blocked- (non-responsive)-to-ABA, of A. angustifolia. We identified 165 mature miRNAs, of which 143 were novel and 22 were conserved plant miRNAs. Seven miRNA conserved families were identified: miR156, miR169, miR394, miR482, miR536, miR1030, and miR1314. Most miRNAs were differentially expressed during the transition from proliferation to the maturation stage of somatic embryogenesis, suggesting that miRNAs play more important roles in the early somatic embryo development. Sixteen were exclusively expressed in RP-RM and 13 in BP-BM transition, indicating that miRNAs are also associated with embryogenic potential. A total of 98 potential target genes were found for 89 miRNAs, involved in post-transcriptional processes, transporters, defense response, sugar regulation, stress, ABA and auxin controlling and signaling, cell-to-cell communication, maintaining suspensor cell identity, brassinosteroids signaling, and cell division. Negative correlations of expression patterns between miRNAs and their targets were detected for miR1030-PRL1, miR1314-ADR1-Like, and Aang34-LRR modules, when analyzed by RT-qPCR. Taken together, our findings provide new insights into the regulatory roles of miRNAs and their target genes in the somatic embryogenesis of Brazilian pine.
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Data availability
Raw sequencing files of sRNAs reads are publicly available and deposited on NCBI under BioProject PRJNA989611.
References
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Acknowledgements
We thank Tiago de Souza and Jonas Gaiarsa (www.taugc.com) for technical support with the bioinformatic analysis, Prof. Dr. Luiz Lehmann Coutinho’s group (Centro de Genômica Funcional, ESALQ/USP) for support with sequencing analysis, in Press (https://inpresscientifica.com.br/) for editing this manuscript, and MSc Amanda F. Macedo (University of São Paulo) for technical support with the experimental analysis.
Funding
This work was supported by the State of Sao Paulo Research Foundation (FAPESP) [2018/08215-0 to L.F.O., 2020/03791-2 to A.R.P.]; the National Council of Technological and Scientific Development (CNPq) [303606/2017-7]; and the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)-Finance Code 001”.
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LFO and EISF contributed to the study conception and design. Material preparation, data collection, and analysis were performed by LFO. LFO and ARP carried out the bioinformatic analysis. The first draft of the manuscript was written by LFO and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
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Communicated by Paloma Moncaleán.
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11240_2023_2576_MOESM2_ESM.xlsx
Supplementary material 2 (XLSX 36 kb) Exclusive and common miRNAs identified among the samples and compared by Venn Diagram (Figure 4C and Supplementary Fig. S4)
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Supplementary material 3 (XLSX 19 kb) Exclusive and common differentially expressed miRNAs identified among the four pairwise comparisons and compared by Venn Diagram (Supplementary Fig. S7)
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Supplementary material 4 (PDF 5341 kb) Predicted secondary structures of conserved miRNAs identified in Araucariaangustifolia, through the Mfold algorithm. The sequences labeled in red or blue correspond to the 5p and 3p, respectively, position in the arm of the hairpin
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Supplementary material 5 (PDF 35314 kb) Predicted secondary structures of novel miRNAs identified in Araucariaangustifolia, through the Mfold algorithm. The sequences labeled in red or blue correspond to the 5p and 3p, respectively, position in the arm of the hairpin
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de Oliveira, L.F., Piovezani, A.R. & Floh, E.I.S. miRNome profiling reveals differential miRNAs associated with embryogenic potential in the somatic embryogenesis of Araucaria angustifolia. Plant Cell Tiss Organ Cult 155, 221–242 (2023). https://doi.org/10.1007/s11240-023-02576-6
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DOI: https://doi.org/10.1007/s11240-023-02576-6