Tropical Plant Biology

, Volume 6, Issue 2–3, pp 117–130 | Cite as

Genome-Wide Analysis of MicroRNAs in Sacred Lotus, Nelumbo nucifera (Gaertn)

  • Yun Zheng
  • Guru Jagadeeswaran
  • Kanchana Gowdu
  • Nian Wang
  • Shaohua Li
  • Ray Ming
  • Ramanjulu Sunkar
Article

Abstract

MicroRNAs (miRNAs) are small non-coding regulatory RNAs that degrade or repress protein synthesis of their messenger RNA targets. This mode of posttranscriptional gene regulation is critical for plant growth and development as well as adaptation to stress conditions. Sacred lotus (Nelumbo nucifera) is a land plant but adapted to the aquatic environment. It is a basal eudicot in the order Proteales, with significant taxonomic importance. Thus identification of miRNAs in sacred lotus could provide information about miRNA evolution, particularly the conservation as well as divergence of miRNAs in dicots. To identify conserved and novel miRNAs in sacred lotus, small RNA libraries from leaves and flowers were sequenced as well as computational strategy was employed. These approaches resulted in identification of 81 miRNAs that can be grouped into 41 conserved/known miRNA families and 52 novel miRNAs forming 49 novel miRNA families. Using 3 mismatches between miRNAs and their mRNA targets as cutoff, we have predicted 137 genes as targets for the conserved and known miRNAs. Overall, this analysis provided a glimpse of miRNA-dependent posttranscriptional gene regulations in sacred lotus.

Keywords

MicroRNAs MicroRNA targets Post-transcriptional gene regulation Sacred lotus Small RNAs 

Abbreviations

AGO

Argonaute

ARF

Auxin response factor

AP2-like

Apetala 2-like transcription factor

CSD

Cu/Zn superoxide dismutase

DCL1

Dicer like-1

GRFs

Growth regulating factors

HD-Zip factors

Homeodomain leucine zipper family of transcription factors

HEN1

Hua Enhancer 1

HYL1

Hyponastic leaves 1

miRNAs

MicroRNAs

NAC factors

NAM, ATAF1/2 and CUC2 domain containing transcription factors

NBS-LRR genes

Nucleoside-binding site leucine rich repeat genes

RISC

RNA-induced silencing complex

RPTM

Reads per ten million

SE

Serrate 1

SPL

Squamosa promoter binding protein-like

tasiRNAs

Trans-acting small interfering RNAs

TCP factors

Teosinte branched 1, Cycloidea, PCF (TCP)-domain protein family

TIR1

Transport inhibitor response 1

Supplementary material

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12042_2013_9127_MOESM3_ESM.pdf (61 kb)
ESM 3(PDF 61 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Yun Zheng
    • 1
    • 2
  • Guru Jagadeeswaran
    • 1
  • Kanchana Gowdu
    • 1
  • Nian Wang
    • 3
  • Shaohua Li
    • 3
  • Ray Ming
    • 4
  • Ramanjulu Sunkar
    • 1
    • 5
  1. 1.Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterUSA
  2. 2.Institute of Developmental Biology and Molecular Medicine, School of Life SciencesFudan UniversityShanghaiChina
  3. 3.Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
  4. 4.Department of Plant BiologyUniversity of Illinois, UIUCUrbana ChampaignUSA
  5. 5.Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterUSA

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