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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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.
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).
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
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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
- Target genes
- Eucalyptus grandis