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A microRNA expression atlas of grapevine based on small RNA library sequencing

ABSTRACT: Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. We analyzed 68 small RNA libraries, which were prepared from a rich and diverse number of tissues (13) harvested on different developmental stages. We identified 110 known miRNAs and annotated 176 novel, some of which belonging to known families and others completely new. We found that very few miRNAs may be defined as tissue specific. However, interestingly, in the stamen 22 miRNAs were found highly specific. Most of the identified miRNAs show low expression levels, whereas, 32 miRNAs are present in all tissues and mainly highly expressed. Additionally, in each organ, the different developmental stages share 30—70% of miRNAs and their modulation leads the regulation of plant development. We also present a target prediction analysis and suggest a first functional description of hundreds of miRNAs. Our findings represent the most complete expression atlas for grapevine and any other woody species, paving the ground for future functional studies.

ORGANISM(S): Vitis vinifera

PROVIDER: GSE59802 | GEO | 2015/05/01

SECONDARY ACCESSION(S): PRJNA256276

REPOSITORIES: GEO

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Project description:Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees. Conclusions: A comprehensive study on M. hupehensis miRNAs related to the juvenile to adult phase transition was performed. The combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.

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A microRNA expression atlas of grapevine based on small RNA library sequencing

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