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.
Highlights
MicroRNAs are a class of endogenous noncoding small RNAs, 20–24 nucleotides, which regulate gene expression at post-transcriptional levels via endonucleolytic cleavage or translational inhibition [1]
To investigate the miRNAs regulatory network during Hami melon fruit development, eight small RNA libraries were constructed from the fruit flesh of Hami melon collected at 10 days after flowering (10DAF), 20 days after flowering (20DAF), 30 days after flowering (30DAF) and 40 days after flowering (40DAF), respectively
The size, sugar content, and organic acid content of Hami melon fruit were closely related to the four developmental stages: 10DAF, 20DAF, 30DAF and 40DAF, and gene expression analysis revealed that the expression patterns were significantly altered from 20DAF to 30DAF [43]
Summary
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]. Ministry of Agriculture of the People’s Republic of China (201203004, http://www.moa.gov.cn/) provided support in the form of salaries for authors HZ, HY, HW, QF, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Xjkjt.gov.cn/) provided support in the form of salaries for authors HZ, GW, XM, ML, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Org.cn/V3/Manage/Login.aspx) provided support in the form of salaries for authors HZ, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of the author are articulated in the ‘author contributions’ section
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