miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Abstract

The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues.We performed deep-sequencing of the small-RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19-25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel-miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.

The draft genome sequence of cork oak

“…The availability of several sets of cork oak high-throughput sequence data, produced with different types of sequencing protocols and in diverse individuals, enabled investigating the performance of the draft genome sequence in read mapping experiments, since these represent the analysis step expected to be most commonly used by other researchers. The available reads were retrieved from NCBI’s Sequence Read Archive (SRA) and were derived from RNA-Seq (generated in the 454 and Illumina platforms) and small RNA-Seq experiments, including the response of cork oak roots to drought 3 , the transcriptomic analysis of male and female flowers 4 , the comparison of good and bad quality cork samples 39 , the response of oak roots to the establishment of ectomycorrhizal symbiosis 2 , the dynamics of cork oak somatic embryogenesis (unpublished results) and miRNA profiling in leaf and cork tissues 40 . Additionally, the RNA-Seq reads derived from the five cork oak tissues were also used, even though this read dataset was derived from samples collected in the tree (HL8) used for genome sequencing.…”

Characterization of the cork oak transcriptome dynamics during acorn development

“…It is possible that the transcript identified in our data has similar functions in the cork oak acorn development. Interestingly, ARF4 is a putative target gene of ta-siRNAs produced from cleavage of the ta-siRNA locus 3 (TAS3) directed by miR390 which was reported as differentially expressed in cork oak tissues [ 104 ].…”

Mass spectrometry‐based forest tree metabolomics

“…RNA‐seq is particular useful for species with extremely large genomes (e.g., conifer megagenomes), and consequently, more‐complex transcriptomes that require a high sequencing depth for suitable transcriptome coverage (Wang, Gerstein, & Snyder, 2009; Baker et al, 2018). The high sequencing depth of RNA‐seq has enabled small RNA discovery and the identification of species‐specific microRNAs in tree species (Sun et al, 2012; Wan et al, 2012; Chaves et al, 2014; Coruh, Shahid, & Axtell, 2014).…”