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MicroRNAs, tasiRNAs, phasiRNAs, and Their Potential Functions in Pineapple

  • Yun Zheng
  • Junqiang Guo
  • Ching Man Wai
  • Ray Ming
  • Ramanjulu Sunkar
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)

Abstract

MicroRNAs are small noncoding RNAs with about 21 nucleotides (nt) that have important functions in both the development and stress responses of plants. Pineapple is an important plant for its agricultural and economical reasons and for its special crassulacean acid metabolism (CAM) photosynthesis system. To better understand the miRNAs and their functions in pineapple, we sequenced three small RNA profiles from flowers, fruits, and leaves, respectively. After analyzing these profiles with bioinformatic methods, 131 conserved miRNAs that could be grouped into 37 families and 16 novel miRNAs were identified. Trans-acting small interfering RNAs (tasiRNAs) are a class of small RNAs that have a different biogenesis pathway but similar functional means by repression of their target genes at different genomic loci. We identified three highly conserved TAS3 loci in pineapple. Recent evidences show that miRNAs also trigger the generations of secondary phased siRNAs (phasiRNAs), from either noncoding genes or coding genes, called as PHAS loci. Our analysis identified 45 PHAS loci encoding 21 nt phasiRNAs and 73 PHAS loci encoding 24 nt phasiRNAs in pineapple. We also predicted the putative targets of the identified miRNAs, tasiRNAs, and phasiRNAs. These results significantly enhance our knowledge of small regulatory RNAs and their potential functions in pineapple.

Keywords

microRNA Pineapple tasiRNA microRNA target phasiRNA PHAS 

Notes

Acknowledgments

The research was supported in part by two grants (No. 31460295 and 31760314) of National Natural Science Foundation of China (http://www.nsfc.gov.cn/) and a grant (No. SKLGE-1511) of the Open Research Funds of the State Key Laboratory of Genetic Engineering, Fudan University, China, to YZ and a grant of Oklahoma Agricultural Experiment Station (http://www.oaes.okstate.edu) to RS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Yun Zheng
    • 1
    • 2
  • Junqiang Guo
    • 2
  • Ching Man Wai
    • 3
  • Ray Ming
    • 3
  • Ramanjulu Sunkar
    • 4
  1. 1.Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingChina
  2. 2.Faculty of Information Engineering and AutomationKunming University of Science and TechnologyKunmingChina
  3. 3.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  4. 4.Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterUSA

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