Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability

Abstract

An increasing number of microRNAs (miRNAs) and miRNA‐related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well‐watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA‐like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24‐nt novel miRNA stood out, were strongly down‐regulated. Given the putative roles of the miRNA‐targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.

Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants

“…While diverse sncRNA profiles have been detected in seed tissues, based mostly on available data from angiosperms, there seems to be a general tendency for a higher abundance and diversity of 24-nt sncRNAs regardless of the developmental stage of the seed [16]. In some gymnosperm species, like maritime pine (Pinus pinaster), 24-nt sncRNAs were also highly expressed in embryos when compared to vegetative tissues [3,17] and more abundant in somatic embryos than in zygotic embryos at equivalent stages of development. In Picea glauca, another gymnosperm species, both 21-nt and 24-nt sncRNAs were abundant in embryos [18], this profile being in contrast to that of buds [19], confirming that the 24-nt sncRNAs are mostly present in reproductive tissues.…”

“…Small non-coding RNAs (sncRNAs) are usually 20-24 nt long RNA molecules with important regulatory functions during development and environmental responses across all groups of land plants, from bryophytes like Physcomitrella patens [1] and Marchantia polymorpha [2], to the gymnosperms [3] and angiosperms [4]. These small molecules are classified into several classes according to their biogenesis and roles [5], the micro RNAs (miRNAs) being the best characterized group of sncRNAs, and the short-interfering RNAs (siRNAs) the other broad category of plant sncRNAs.…”

MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode

“…Part of the miRNA families here detected as differentially expressed after PWN inoculation were also responsive to drought stress in P. pinaster 23 (miR159, miR164, miR166, miR169, miR396, miR529, miR1313, miR3627, miRnovel578), suggesting these families may have a role in the regulation of stress responses in general.…”

“…Plant hormone signalling genes were targeted by differentially expressed miRNAs, leading to the suppression of indole acetic acid and zeatin synthesis thus causing the inhibition of plant growth, but the role of the expressed miRNAs in regulating plant immune response was not addressed. In P. pinaster , sRNAs were reported to be involved in the regulation of embryo development 22 and abiotic stress response 23 , but their function in biotic stress has not been described.…”

Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA–miRNA–mRNA Network in White Spruce

“…In conifers, miRNAs related to somatic embryogenesis have been studied on larch [30], Norway spruce [31], and Picea balfouriana [32]. Stress-related miRNAs were also reported in Sabina chinensis [33] and Pinus pinaster [34]. Unfortunately, the study of lncRNAs on the stress response and somatic embryogenesis has not been reported in conifers at present.…”