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, 251:47 | Cite as

Identification and characterization of circular RNAs during wood formation of poplars in acclimation to low nitrogen availability

  • Huimin Liu
  • Wanwen Yu
  • Jiangting Wu
  • Zhuorong Li
  • Hui Li
  • Jing Zhou
  • Jingjing Hu
  • Yan LuEmail author
Original Article
  • 75 Downloads

Abstract

Main conclusion

Circular RNA (circRNA) identification and expression profiles, and construction of circRNAs-miRNAs-mRNAs networks indicates that circRNAs are involved in wood formation of poplars in acclimation to low nitrogen availability.

Abstract

Circular RNAs (circRNAs) are covalently closed non-coding RNAs that play pivotal roles in various biological processes. However, circRNAs’ roles in wood formation of poplars in acclimation to low nitrogen (N) availability are currently unknown. Here, we undertook a systematic identification and characterization of circRNAs in the wood of Populus × canescens exposed to either 50 (low N) or 500 (normal N) µM NH4NO3 using rRNA-depleted RNA-sequencing. A total of 2,509 unique circRNAs were identified, and 163 (ca. 6.5%) circRNAs were significantly differentially expressed (DE) under low N condition. We observed a positive correlation between the expression patterns of DE circRNAs and their hosting protein-coding genes. Moreover, circRNAs–miRNAs–mRNAs’ networks were identified in the wood of poplars under low N availability. For instance, upregulated several circRNAs, such as circRNA1226, circRNA 1732, and circRNA392 induced increases in nuclear factor Y, subunit A1-A (NFYA1-A), NFYA1-B, and NFYA10 transcript levels via the mediation of miR169b members, which is in line with reduced xylem width and cell layers of the xylem in the wood of low N-supplied poplars. Upregulation of circRNA1006, circRNA1344, circRNA1941, circRNA901, and circRNA146 caused increased transcript level of MYB61 via the mediation of a miR5021 member, corresponding well to the higher lignin concentration in the wood of low N-treated poplars. Overall, these results indicated that DE circRNAs play an essential role in regulating gene expression via circRNAs–miRNAs–mRNAs’ networks to modulate wood anatomical and chemical properties of poplars in acclimation to low N availability.

Keywords

ceRNA networks Circular RNA Low nitrogen Populus Secondary xylem 

Abbreviations

CSLG3

Cellulose synthase-like G3

P5CS1

Delta1-pyrroline-5-carboxylate synthase 1

DE

Differentially expressed

GO

Gene Ontology

MYB61

MYB domain protein 61

NFYA1-A/1-B/10

Nuclear factor Y, subunit A1-A/1-B/10

Notes

Acknowledgements

This study was jointly supported by the Key Forestry Public Welfare Project (201504105), the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (No. CAFYBB2016QB005), the Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF) (No. CX(16)1005), and the National Natural Science Foundation of China (No. 31500507).

Compliance with ethical standards

Conflict of interest

The authors have no conflicts of interest to declare.

Supplementary material

425_2020_3338_MOESM1_ESM.xlsx (902 kb)
Supplementary file1 (XLSX 901 kb)
425_2020_3338_MOESM2_ESM.docx (1.5 mb)
Supplementary file2 (DOCX 1517 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2020

Authors and Affiliations

  1. 1.State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement and Utilization of State Forestry and Grassland Administration, Non-Timber Forest Research and Development CenterChinese Academy of ForestryZhengzhouChina
  2. 2.Co-Innovation Center for the Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
  3. 3.State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of ForestryChinese Academy of ForestryBeijingChina
  4. 4.State Key Laboratory of Tree Genetics and Breeding, Research Institution of Tropical ForestryChinese Academy of ForestryGuangzhouChina
  5. 5.Inertia Shanghai Biotechnology Co., Ltd.ShanghaiChina

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