Identification of novel miRNAs and their target genes in Eucalyptus grandis
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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.
KeywordsmiRNA Target genes Eucalyptus grandis Function MIR396
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).
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29CrossRefPubMedPubMedCentralGoogle Scholar
- Baucher M, Moussawi J, Vandeputte OM, Monteyne D, Mol A, Perez-Morga D, El JM (2013) A role for the miR396/GRF network in specification of organ type during flower development, as supported by ectopic expression of Populus trichocarpa miR396c in transgenic tobacco. Plant Biol (Stuttg) 15:892–898CrossRefGoogle Scholar
- Dehury B, Panda D, Sahu J, Sahu M, Sarma K, Barooah M, Sen P, Modi M (2013) In silico identification and characterization of conserved miRNAs and their target genes in sweet potato (Ipomoea batatas L.) expressed sequence tags (ESTs). Plant Signal Behav 8:e26543CrossRefPubMedPubMedCentralGoogle Scholar
- Levy A, Szwerdszarf D, Abu-Abied M, Mordehaev I, Yaniv Y, Riov J, Arazi T, Sadot E (2014) Profiling microRNAs in Eucalyptus grandis reveals no mutual relationship between alterations in miR156 and miR172 expression and adventitious root induction during development. BMC Genomics 15:524CrossRefPubMedPubMedCentralGoogle Scholar
- Muñoz-Espinoza C, Di Genova A, Correa J, Silva R, Maass A, Gonzalez-Aguero M, Orellana A, Hinrichsen P (2016) Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. BMC Plant Biol 16:104CrossRefPubMedPubMedCentralGoogle Scholar
- Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Kulheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J (2014) The genome of Eucalyptus grandis. Nature 510:356–362CrossRefPubMedGoogle Scholar
- Pappas M, Reis A, Farinell L, Pasquali G, Jr PG, Grattapaglia D (2011) Interspecific discovery and expression profiling of Eucalyptus micro RNAs by deep sequencing. BMC Proc 5:1–2Google Scholar