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Identification of novel miRNAs and their target genes in Eucalyptus grandis

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Abstract

Despite Eucalyptus grandis being the most widely planted hardwood tree globally, along with the availability of a sequenced genome and easily accessible functional genetic tools, the quantities and roles of miRNA in its developmental processes remains largely unknown. In this study, we constructed small RNA libraries by high-throughput sequencing from Eucalyptus grandis samples, and 386 novel miRNAs were identified by miRDeep2. We found 179 novel miRNAs, 41 miRNA families, and 456 target genes in leaf samples, and 257 novel miRNAs, 61 miRNA families, and 483 target genes in stem samples. The function of the MIR396 family of miRNAs in Eucalyptus grandis was found to be mainly associated with the process of cell growth. By annotation analysis of miRNA targets, we found that some target genes, such as GRF, expansin-A15, and RPS2, had a close correlation in stem. Finally, the three randomly selected members of the MIR396 family were confirmed to express in Eucalyptus grandis by qRT-PCR, indicating that our reported miRNAs were existed. The identification of miRNAs and their target genes will lead to a greater understanding of the role of miRNAs in the physiology, growth, and development of Eucalyptus grandis trees.

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Acknowledgements

We thank Xianhai Zhao, Junbo He (South China Agricultural University) for critical discussion and suggestions. Chunjie Fan and Bingshan Zeng from the Research Institute of tropical forestry, Chinese Academy of Forestry, Guangzhou, presented the Eucalyptus plant.

Funding

This work was supported by the Open Fund of State Key Laboratory of Tree Genetics and Breeding (Beijing) (Grant Number TGB2015007), the National Key Research and Development Program of China (Grant Number 2016YFD0600105), and the National Natural Science Foundation of China (Grant Number 31670601, 31670670).

Author information

Correspondence to Ai-Min Wu.

Additional information

Data archiving statement

The collection of small RNA sequences generated in this study is available under NCBI’s BioProject accession PRJNA382281 and NCBI’s Sequence Read Archive (SRA) database (accession numbers SRR5433936 and SRR5433935), under BioSample accession numbers SAMN06703134 and SAMN06703135.

Communicated by A. Brunner

Electronic supplementary material

Fig. S1
figure4

Picture of a 5-month-old Eucalyptus grandis tree planted in a growth room at 25 °C and watered once every two days with tap water (a), the magnification of the leaf (b), and cross-section of the stem’s radius with phloroglucinol dye (c) were both shown (PNG 2.20 MB)

Fig. S2
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The secondary structure of eu-MIR396e, a member in MIR396 family. The red color represents the mature sequence, the yellow color represents the cycle structure, and the blue color represents the star sequence. (PNG 31.4 KB)

Fig. S3
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The miRNAs of leaf and stem. The green color represents the miRNAs number in stem, the purple color represents the miRNAs number in leaf, and the blue color represents the common miRNAs number in leaf and stem. (PNG 76.2 KB)

Fig. S4
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The relative expression of MIR396 family members in different tissues. The horizontal axis represented different miRNA in the MIR396 family, the vertical axis was the relative expression of miRNA. The errror bars are standard deviations. (PNG 59.5 KB)

Fig. S5
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The phylogenetic tree of the MIR396 family. The samples are from Arabidopsis thaliana (two members), Nicotiana tabacum (three members), Populus trichocarpa (seven members), and Eucalyptus grandis (11 members). (PNG 630 KB)

Fig. S6
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The Biological Process of the target genes in all, conserved and non-conserved miRNAs in leaf(a) and stem(b). (PNG 381 KB)

Fig. S7
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The Cellular Component of the target genes in all, conserved and non-conserved miRNAs in leaf(a) and stem(b). (PNG 235 KB)

Fig. S8
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The Molecular Function of the target genes in all, conserved and non-conserved miRNAs in leaf(a) and stem(b). (PNG 272 KB)

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Lin, Z., Li, Q., Yin, Q. et al. Identification of novel miRNAs and their target genes in Eucalyptus grandis. Tree Genetics & Genomes 14, 60 (2018). https://doi.org/10.1007/s11295-018-1273-x

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Keywords

  • miRNA
  • Target genes
  • Eucalyptus grandis
  • Function
  • MIR396