Identification and characterization of circular RNAs during wood formation of poplars in acclimation to low nitrogen availability
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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.
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.
KeywordsceRNA networks Circular RNA Low nitrogen Populus Secondary xylem
Cellulose synthase-like G3
Delta1-pyrroline-5-carboxylate synthase 1
MYB domain protein 61
Nuclear factor Y, subunit A1-A/1-B/10
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.
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