Identification and Characterization of MicroRNAs in Ginkgo biloba var. epiphylla Mak

Abstract

Ginkgo biloba, a dioecious plant known as a living fossil, is an ancient gymnosperm that stands distinct from other gymnosperms and angiosperms. Ginkgo biloba var. epiphylla (G. biloba var. epiphylla), with ovules borne on the leaf blade, is an unusual germplasm derived from G. biloba. MicroRNAs (miRNAs) are post-transcriptional gene regulators that play critical roles in diverse biological and metabolic processes. Currently, little is known about the miRNAs involved in the key stage of partly epiphyllous ovule germination in G. biloba var. epiphylla. Two small RNA libraries constructed from epiphyllous ovule leaves and normal leaves of G. biloba var. epiphylla were sequenced on an Illumina/Solexa platform. A total of 82 miRNA sequences belonging to 23 families and 53 putative novel miRNAs were identified in the two libraries. Differential expression analysis showed that 25 conserved and 21 novel miRNAs were differentially expressed between epiphyllous ovule leaves and normal leaves. The expression patterns of partially differentially expressed miRNAs and the transcript levels of their predicted target genes were validated by quantitative real time RT-PCR. All the expression profiles of the 21 selected miRNAs were similar to those detected by Solexa deep sequencing. Additionally, the transcript levels of almost all the putative target genes of 9 selected miRNAs were opposite to those of the corresponding miRNAs. The putative target genes of the differentially expressed miRNAs were annotated with Gene Ontology terms related to reproductive process, metabolic process and responding to stimulus. This work presents a broad range of small RNA transcriptome data obtained from epiphyllous ovule and normal leaves of G. biloba var. epiphylla, which may provide insights into the miRNA-mediated regulation in the epiphyllous ovule germination process.

Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia

“…This type of cultivar had previously only been reported growing in Japan. The obtained results are in line with the finding of Zhang et al (2015) who identified a total of 82 miRNA sequences belonging to 23 families and 53 putative novel miRNAs. The expression analysis showed that 25 conserved and 21 novel miR-NAs were differentially expressed between epiphyllous ovule leaves and normal leaves.…”

Discovery and Profiling of microRNAs at the Critical Period of Sex Differentiation in Xanthoceras sorbifolium Bunge

“…Therefore, regulating the MicroRNAs (miRNAs) are a class of endogenous non-coding sRNAs with a size of 21-24 nucleotides (nt) that widely exist in eukaryotes [20,21]. As a negative regulator of gene expression, miRNAs play critical roles in the transcriptional and post-transcriptional regulation of many genes related to plant growth and developmental processes, such as organ morphogenesis, phase change, fruit development, defense against stress, hormone synthesis, and signal transduction [22][23][24][25][26]. In addition, some miRNAs have been identified to play a role in sex determination in plants.…”

Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microRNA repertoire in land plants

“…The miRNAs of M. quadrifolia and seed plants identified by Chávez-Montes et al [19] were reanalysed to identify bona fide conserved miRNAs (see Materials and Methods). We also compared P. minima sequences with the miRNAs of various gymnosperms and basal angiosperms [19,[30][31][32][33], as well as conserved miRNAs identified recently in the liverworts Pellia endiviifolia [34] and Marchantia polymorpha [35,36].…”