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Identification of microRNA-like RNAs from Curvularia lunata associated with maize leaf spot by bioinformation analysis and deep sequencing

Abstract

Deep sequencing of small RNAs is a useful tool to identify novel small RNAs that may be involved in fungal growth and pathogenesis. In this study, we used HiSeq deep sequencing to identify 747,487 unique small RNAs from Curvularia lunata. Among these small RNAs were 1012 microRNA-like RNAs (milRNAs), which are similar to other known microRNAs, and 48 potential novel milRNAs without homologs in other organisms have been identified using the miRBase© database. We used quantitative PCR to analyze the expression of four of these milRNAs from C. lunata at different developmental stages. The analysis revealed several changes associated with germinating conidia and mycelial growth, suggesting that these milRNAs may play a role in pathogen infection and mycelial growth. A total of 8334 target mRNAs for the 1012 milRNAs that were identified, and 256 target mRNAs for the 48 novel milRNAs were predicted by computational analysis. These target mRNAs of milRNAs were also performed by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. To our knowledge, this study is the first report of C. lunatas milRNA profiles. This information will provide a better understanding of pathogen development and infection mechanism.

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Acknowledgments

The assistance of Dr. Wayne Borth in preparation of the manuscript is gratefully acknowledged. This work was funded by the National Natural Science Foundation of China (Grant Nos. 31272026 and 31301611) and Open project of State Key Laboratory of Crop Stress Biology in Arid Regions (CSBAA2011-18).

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Correspondence to Jumei Hou.

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The authors declare that they have no conflicts of interest.

This article does not contain any studies performed by any of the authors on human participants or animals.

Additional information

Communicated by J. Perez-Martin.

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Liu, T., Hu, J., Zuo, Y. et al. Identification of microRNA-like RNAs from Curvularia lunata associated with maize leaf spot by bioinformation analysis and deep sequencing. Mol Genet Genomics 291, 587–596 (2016). https://doi.org/10.1007/s00438-015-1128-1

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Keywords

  • Curvularia lunata
  • HiSeq deep sequencing
  • Small RNA
  • milRNA