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

PLoS One. 2017 Jul 24;12(7):e0180600. doi: 10.1371/journal.pone.0180600. eCollection 2017.

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.

Publication types

  • Validation Study

MeSH terms

  • Conserved Sequence
  • Cucurbitaceae / genetics*
  • Cucurbitaceae / growth & development*
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Gene Ontology
  • Genome-Wide Association Study
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / genetics*
  • Nucleic Acid Amplification Techniques
  • RNA, Plant / genetics*
  • Real-Time Polymerase Chain Reaction
  • Sequence Analysis, RNA

Substances

  • MicroRNAs
  • RNA, Plant

Grants and funding

ABLife, Inc. provided in the form of salaries for authors LY, YZ, 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 these authors are articulated in the ‘author contributions’ section. National Natural Science Foundation of China (31160395, http://www.nsfc.gov.cn) provided support in the form of salaries for authors HZ, HW, 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 these authors are articulated in the ‘author contributions’ section. 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. The specific roles of these authors are articulated in the ‘author contributions’ section. Science & Technology Department of Xinjiang Uygur Autonomous Region (KY2014024, http://www.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. The specific roles of these authors are articulated in the ‘author contributions’ section. China Postdoctoral Science Foundation (131620, http://bg.chinapostdoctor.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.