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Investigating the MicroRNAomes of Two Developmental Phases of Dendrocalamus latiflorus (Poaceae: Bambusoideae) Inflorescences

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Abstract

Plant microRNAs (miRNAs) play important roles in various developmental and physiological processes (e.g. seed germination, vegetative growth, flowering, seed production, and responses to abiotic or biotic stimuli) by targeting mRNAs for cleavage or translational repression at the post-transcriptional level. Bamboo flowering is an unusual physiological phenomenon relative to the typical graminaceous plants. In this study, we focused on the microRNAome of developing Dendrocalamus latiflorus inflorescences. Solexa high-throughput small RNA (sRNA) sequencing technology was used to sequence and quantify the miRNAs expressed during two phases of D. latiflorus flower development. A total of 118 conserved miRNAs and 47 novel miRNAs was identified in the developing flowers. The transcript levels of most of the miRNAs were similar between the two phases. However, five miRNAs showed distinct changes as the flowering developed, with the novel miRNA dla-miR18 in particular showing a large difference in transcript abundance between the two phases. Fifteen of the D. latiflorus miRNAs found in this study appeared likely to be specific to flower development. Moreover, 130 of the floral unigenes of D. latiflorus were determined to be putative targets of the miRNAs, and the miRNA cleavage sites of seven of these putative targets were validated by 5′-RACE. The results of this study provide the first broad survey of the microRNAomes of Bambusoideae and yield valuable insights into the potential roles of microRNAs in bamboo inflorescence development. Our findings represent a starting point for future functional research on the role of miRNA in the flower development in D. latiflorus and related species.

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Abbreviations

AGO:

Argonaute

ath:

Arabidopsis thaliana

bdi:

Brachypodium distachyon

DCL:

Dicer-like

dla:

Dendrocalamus latiflorus

gma:

Glycine max

miRNA:

microRNA

nat-miRNA:

Natural antisense microRNA

NGS:

Next generation sequencing

osa:

Oryza sativa

ptc:

Populus trichocarpa

qRT-PCR:

Quantitative RT-PCR

RACE:

Rapid amplification of complementary DNA ends

sbi:

Sorghum bicolor

siRNA:

Small interfering RNA

sRNA:

Small RNA

tasiRNA:

Transacting siRNA

zma:

Zea mays

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. U1136603,31470322,30990244) and the Western Light Talent Culture Project of the Chinese Academy of Sciences (No. 2010312D11035). We thank Ms. Xian-Lun Yin of Kunming Institute of Botany, Chinese Academy of Science for her help with the biological experiments; Xing-Jun Wang from High-Tech Research Center, Shandong Academy of Agricultural Sciences and Dr. Andreas Schreiber from Australian Centre for Plant Functional Genomics, University of Adelaide for technical advice and Dr. Larson-Rabin Zachary visiting scientist to Kunming Institute of Botany from the University of Wisconsin for revision of the manuscript.

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Authors and Affiliations

  1. Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species (GBOWS), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China

    Xu-Yao Zhao, Xiao-Yan Wang, Lei Zhao, Xue-Mei Zhang, Si-Yun Chen, Peng-Fei Ma, Xiang-Yang Hu, De-Zhu Li & Zhen-Hua Guo

  2. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China

    Xu-Yao Zhao, Xiao-Yan Wang, Lei Zhao, Xue-Mei Zhang, Si-Yun Chen, Peng-Fei Ma, De-Zhu Li & Zhen-Hua Guo

  3. Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China

    Xu-Yao Zhao & Xiao-Yan Wang

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  1. Xu-Yao Zhao
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Correspondence to De-Zhu Li or Zhen-Hua Guo.

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Xu-Yao Zhao and Xiao-Yan Wang contributed equally to this work.

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Additional file 1

Primers used in this study (DOCX 21 kb)

Additional file 2

miRNAs suspected of being technical variants: those miRNAs with an abundance of less than 0.12% of the most abundant possible parent sequence, and their possible parent sequence will always be highly conserved members of the same miRNA families (DOCX 17 kb)

Additional file 3

All identified known miRNAs in D. latiflorus. Abbreviations: dla, Dendrocalamus latiflorus; ath, Arabidopsis thaliana; bdi, Brachypodium distachyon; osa, Oryza sativa; zma, Zea mays (DOCX 30 kb)

Additional file 4

Known monocot-specific miRNAs (DOCX 16 kb)

Additional file 5

New members of MIRfam2275 (DOCX 17 kb)

Additional file 6

Evolutionary tree built from conserved miRNA genes (DOCX 21 kb)

Additional file 7

All predicted novel miRNAs in D. latiflorus (DOCX 27 kb)

Additional file 8

Dissolution curves of U6 SnRNA and 17 miRNAs (GIF 23 kb)

High resolution (TIFF 2007 kb)

Additional file 9

Targets of all known miRNAs and novel miRNAs (XLSX 24 kb)

Additional file 10

Conserved miRNA expression difference between two phases (DOCX 16 kb)

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Zhao, XY., Wang, XY., Zhao, L. et al. Investigating the MicroRNAomes of Two Developmental Phases of Dendrocalamus latiflorus (Poaceae: Bambusoideae) Inflorescences. Plant Mol Biol Rep 33, 1141–1155 (2015). https://doi.org/10.1007/s11105-014-0808-z

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