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

Scientific Reports
Andreia S RodriguesCélia M Miguel

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 develop...Continue Reading

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Citations

Feb 23, 2020·International Journal of Molecular Sciences·Anna M WójcikMałgorzata D Gaj
Apr 1, 2020·International Journal of Molecular Sciences·Barbara WójcikowskaMałgorzata D Gaj
Jul 18, 2020·International Journal of Molecular Sciences·Anna Maria Wójcik

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Methods Mentioned

BETA
RNA-Seq
Assay

Software Mentioned

REViGO
Cytoscape
psRNAtarget
R
pheatmap
miRPursuit

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