Research Article: Genome-wide identification of Hami melon miRNAs with putative roles during fruit development

Date Published: July 24, 2017

Publisher: Public Library of Science

Author(s): Hong Zhang, Lan Yin, Huaisong Wang, Guangzhi Wang, Xinli Ma, Meihua Li, Haibo Wu, Qiushi Fu, Yi Zhang, Hongping Yi, Turgay Unver.

http://doi.org/10.1371/journal.pone.0180600

Abstract

MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, “transcription, DNA-dependent”, “rRNA processing”, “oxidation reduction”, “signal transduction”, “regulation of transcription, DNA-dependent”, and “metabolic process” were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5’ RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices.

Partial Text

MicroRNAs are a class of endogenous noncoding small RNAs, 20–24 nucleotides (nt), which regulate gene expression at post-transcriptional levels via endonucleolytic cleavage or translational inhibition [1]. In plants, the primary miRNA transcripts are first transcribed by RNA polymerase II and processed by Dicer-like 1 to generate stem-loop miRNA:miRNA* duplex [2]. Then, the duplex disassociates and mature miRNAs are incorporated to the RNA-induced silencing complex. Argonaute proteins are a core component of this complex, which could bind to the small RNAs and enzymatically cleave the complementary mRNAs or inhibit its translation [1, 3].

In the present study, we performed a close examination of the dynamic regulation of miRNAs during sequential stages of Hami melon fruit development. Our results revealed that specific miRNAs were differentially regulated during fruit development, and therefore may play important roles in fruit growth and ripening. All the related regulatory events maybe contributing in a balanced manner to the process of normal Hami fruit development and ripening. The findings of this study could be used for further research and applications in breeding practices. Ripening-associated transcription factors, NAC, SPL, AP2, HD-ZIP III, and ARF, were predicted as the targets of developmentally regulated miRNAs in Hami melon, further investigation on how miRNAs and ripening-associated transcription factors interact during the programmed process of fruit ripening may help us find the key factors that determine the long shelf life of Hami melon.

 

Source:

http://doi.org/10.1371/journal.pone.0180600

 

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