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Open AccessArticle

Genome-Wide Analysis of the miRNA–mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra

1
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
2
College of Life Science, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(6), 430; https://doi.org/10.3390/genes10060430
Received: 9 April 2019 / Revised: 21 May 2019 / Accepted: 31 May 2019 / Published: 5 June 2019
(This article belongs to the Special Issue Plant miRNA Mediated Defense Response)
Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance. View Full-Text
Keywords: Populus simonii × P. nigra; cold induction; microRNAs; transcriptome Populus simonii × P. nigra; cold induction; microRNAs; transcriptome
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Zhou, B.; Kang, Y.; Leng, J.; Xu, Q. Genome-Wide Analysis of the miRNA–mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra. Genes 2019, 10, 430.

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    Link: http://Figure S1, Figure S2, Figure S3, Figure S4
    Description: Figure S1 Transcripts annotated in the databases of NR, NT, PFAM, GO and KOG Figure S2 Distribution of unigenes assigned to different plant species in a BLASTX search of the NR protein database. Different colors indicate different species; the number of unigenes for each species is given in square brackets. Figure S3 Significantly enriched GO terms in the up and down-regulated transcripts ranked according to the p-value and number of genes. Figure S4 Recovery growth after treatment with different low temperature and time
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