Abstract
As one of the largest members of Poaceae family, bamboo is a very important agricultural plant in the world. The development of bamboo shoot is very special and particularly significant to bamboo production. Understanding the developmental differences between bamboo shoot and rhizome shoot is extremely valuable for us to further elucidate the mechanism of bamboo shoot formation since both bamboo shoot and rhizome shoot develop directly from rhizome bud underground. In this paper, miRNA chips with 413 miRNA probes were used to compare miRNA expressions between bamboo shoot and rhizome shoot. The experiment revealed 64 bamboo shoot upregulated and 56 rhizome shoot up-regulated miRNAs which were classified into four major categories according to deep sequencing based target prediction. Meristem and morphological development related miRNAs were most important in bamboo shoot, especially miR171 and miR156 members. While in rhizome shoot the mainstream of miRNA expressions was metabolism and nutrition related ones, especially miR395 members. The meristem and morphological development related miRNAs in bamboo shoot showed some embryonic characteristics and suggested the participation of several phytohormones like gibberellin, cytokinin and auxin, which were absent in those miRNAs of rhizome shoot. Further qRT-PCR detections of 21 up-regulated miRNAs in bamboo seedlings indicated that 12 ones were regulated to varying degrees by some environmental factors. Among them, rhizome shoot upregulated osa-miR395b was the most environment-sensitive miRNA, particularly to dehydration. And the bamboo shoot up-regulated osa-miR399j proved uniquely and strongly induced by phosphor. The existence of multiple regulation sites from same miRNA suggested the probability of crosstalks among meristem development, metabolism and stress response during bamboo shoot and rhizome shoot development.
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References
Baldwin KL, Dinh EM, Hart BM, Masson PH (2013) CACTIN is an essential nuclear protein in Arabidopsis and may be associated with the eukaryotic spliceosome. FEBS Lett 587:873–879
Chiu WB, Lin CH, Chang CJ, Hsieh MH, Wang AY (2006) Molecular characterization and expression of four cDNAs encoding sucrose synthase from green bamboo Bambusa oldhamii. New Phytol 170:53–63
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159
Dello IR, Linhares FS, Scacchi E, Casamitjana-Martinez E, Heidstra R, Costantino P, Sabatini S (2007) Cytokinins determine Arabidopsis root-meristem size by controlling cell differentiation. Curr Biol 17:678–682
Frazier TP, Sun G, Burklew CE, Zhang B (2011) Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol Biotechnol 49:159–165
Gao J, Ge W, Zhang Y, Cheng Z, Li L, Hou D, Hou C (2015) Identification and characterization of microRNAs at different flowering developmental stages in moso bamboo (Phyllostachys edulis) by high-throughput sequencing. Mol Genet Genomics 290:2335–2353
Gao M, Li X, Huang J, Gropp GM, Gjetvaj B, Lindsay DL, Wei S, Coutu C, Chen Z, Wan X, Hannoufa A, Lydiate DJ, Gruber MY, Chen ZJ, Hegedus DD (2015) SCARECROW-LIKE15 interacts with HISTONE DEACETYLASE19 and is essential for repressing the seed maturation programme. Nat Commun 6:7243
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652
Guddeti S, Zhang DC, Li AL, Leseberg CH, Kang H, Li XG, Zhai WX, Johns MA, Mao L (2005) Molecular evolution of the rice miR395 gene family. Cell Res 15:631–638
He CY, Cui K, Zhang JG, Duan AG, Zeng YF (2013) Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo. BMC Plant Biol 13:119
Huang J, Liu L, Zhang B, Qiu L (2002) Dynamic changes of endophytohormone in rhizomal buds of Phyllostachys praecox. Scientia Silvae Sinicae 38:38–41
Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544
Li D, Wang Z, Zhu Z, Xi N, Jia L, Guo Z, Yang G, Chris S (2006) Flora of China, Vol 22. Science Press and Missouri Botanical Garden Press, Beijing and St. Louis
Lin EP, Peng HZ, Jin QY, Deng MJ, Li T, Xiao XC, Hua XQ, Wang KH, Bian HW, Han N, Zhu MY (2009) Identification and characterization of two bamboo (Phyllostachys praecox) AP1/SQUA-like MADS-box genes during floral transition. Planta 231:109–120
Ma Z, Hu X, Cai W, Huang W, Zhou X, Luo Q, Yang H, Wang J, Huang J (2014) Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions. PLoS Genet 10: e1004519
Matthewman CA, Kawashima CG, Huska D, Csorba T, Dalmay T, Kopriva S (2012) miR395 is a general component of the sulfate assimilation regulatory network in Arabidopsis. FEBS Lett 586: 3242–3248
Moubayidin L, Perilli S, Dello IR, Di Mambro R, Costantino P, Sabatini S (2010) The rate of cell differentiation controls the Arabidopsis root meristem growth phase. Curr Biol 20:1138–1143
Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, Kurata N (2007) A Germ Cell-CSpecific Gene of the ARGONAUTE Family Is Essential for the Progression of Premeiotic Mitosis and Meiosis during Sporogenesis in Rice. Plant Cell 19:2583–2594
Ogas J, Kaufmann S, Henderson J, Somerville C (1999) PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Proc Natl Acad Sci USA 96:13839–13844
Peng HZ, Lin EP, Sang QL, Yao S, Jin QY, Hua XQ, Zhu MY (2007) Molecular cloning, expression analyses and primary evolution studies of REV-and TB1-like genes in bamboo. Tree Physiol 27: 1273–1281
Peng Z, Lu Y, Li L, Zhao Q, Feng Q, Gao Z, Lu H, Hu T, Yao N, Liu K, Li Y, Fan D, Guo Y, Li W, Lu Y, Weng Q, Zhou C, Zhang L, Huang T, Zhao Y, Zhu C, Liu X, Yang X, Wang T, Miao K, Zhuang C, Cao X, Tang W, Liu G, Liu Y, Chen J, Liu Z, Yuan L, Liu Z, Huang X, Lu T, Fei B, Ning Z, Han B, Jiang Z (2013) The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat Genet 45:456–461
Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110:513–520
Smertenko A, Bozhkov PV (2014) Somatic embryogenesis: life and death processes during apical-basal patterning. J Exp Bot doi:10.1093/jxb/eru005
Sun YH, Shi R, Zhang XH, Chiang VL, Sederoff RR (2012) MicroRNAs in trees. Plant Mol Biol 80:37–53
Ullrich TC, Blaesse M, Huber R (2001) Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation. EMBO J 20:316–329
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:H34
Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3:12
Wang K, Peng H, Lin E, Jin Q, Hua X, Yao S, Bian H, Han N, Pan J, Wang J, Deng M, Zhu M (2010) Identification of genes related to the development of bamboo rhizome bud. J Exp Bot 61:551–561
Wang K, Peng H, Lin E, Jin Q, Hua X, Yao S, Bian H, Han N, Pan J, Wang J, Deng M, Zhu M (2010) Identification of genes related to the development of bamboo rhizome bud. J Exp Bot 61:551–561
Wang Y, Xu L, Chen Y, Shen H, Gong Y, Limera C, Liu L (2013) Transcriptome profiling of radish (Raphanus sativus L. root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing. PLoS One 8:e66539
Xu P, Mohorianu I, Yang L, Zhao H, Gao Z, Dalmay T (2014) Small RNA profile in moso bamboo root and leaf obtained by high definition adapters. PLoS One 9:e103590
Zhang Z, Hu C, Jin A (1996) Observation of the morphology and the structure of phyllostachys praecox rhizome lateral bud developing into shoot. J Bamboo Res 15:60–66
Zhao B, Ge L, Liang R, Li W, Ruan K, Lin H, Jin Y (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Mol Biol 10:29
Zhao H, Chen D, Peng Z, Wang L, Gao Z (2013) Identification and characterization of microRNAs in the leaf of ma bamboo (Dendrocalamus latiflorus) by deep sequencing. PLoS One 8: e78755
Zhao H, Wang L, Dong L, Sun H, Gao Z (2014) Discovery and Comparative Profiling of microRNAs in Representative Monopodial Bamboo (Phyllostachys edulis) and Sympodial Bamboo (Dendrocalamus latiflorus). PLoS One 9:e102375
Zhou FC (1998) Cultivation and utilization of bamboo. Bamboo Research 93–99
Zhou L, Liu Y, Liu Z, Kong D, Duan M, Luo L (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168
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Jin, QY., Peng, HZ., Lin, EP. et al. Identification and characterization of differentially expressed miRNAs between bamboo shoot and rhizome shoot. J. Plant Biol. 59, 322–335 (2016). https://doi.org/10.1007/s12374-015-0581-z
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DOI: https://doi.org/10.1007/s12374-015-0581-z