Chen X. Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol. 2009;25:21–44.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, et al. Transcriptome-wide identification of microRNA targets in rice. Plant J. 2010;62:742–59.
Article
CAS
PubMed
Google Scholar
Martinez G, Forment J, Llave C, Pallas V, Gomez G. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS One. 2011;6:e19523.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie F, Frazier TP, Zhang B. Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta. 2010;232:417–34.
Article
CAS
PubMed
Google Scholar
Chuck G, Candela H, Hake S. Big impacts by small RNAs in plant development. Curr Opin Plant Biol. 2009;12:81–6.
Article
CAS
PubMed
Google Scholar
Ruiz-Ferrer V, Voinnet O. Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol. 2009;60:485–510.
Article
CAS
PubMed
Google Scholar
Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett. 2006;580:3753–62.
Article
CAS
PubMed
Google Scholar
Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet. 2004;36:1282–90.
Article
CAS
PubMed
Google Scholar
Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One. 2007;2:e219.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 2008;8:25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, et al. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res. 2008;18:1602–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, et al. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009;5:e1000716.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xu MY, Dong Y, Zhang QX, Zhang L, Luo YZ, Sun J, et al. Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genomics. 2012;13:421.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang F, Li L, Liu L, Li H, Zhang Y, Yao Y, et al. High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L ssp pekinensis). Mol Gen Genomics. 2012;287:555–63.
Article
CAS
Google Scholar
Zhang W, Luo Y, Gong X, Zeng W, Li S. Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem. 2009;33:84–93.
Article
CAS
PubMed
Google Scholar
Zhang N, Yang J, Wang Z, Wen Y, Wang J, He W, et al. Identification of novel and conserved microRNAs related to drought stress in potato by deep sequencing. PLoS One. 2014;9:e95489.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hu CD, Liang YZ, Guo FQ, Li XR, Wang WP. Determination of essential oil composition from Osmanthus fragrans tea by GC-MS combined with a chemometric resolution method. Molecules. 2010;15:3683–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liao X, Hu F, Chen Z. Identification and quantitation of the bioactive components in Osmanthus fragrans fruits by HPLC-ESI-MS/MS. J Agric Food Chem. 2018;66:359–67.
Article
CAS
PubMed
Google Scholar
Wang Y, Zhang C, Dong B, Fu J, Hu S, Zhao H. Carotenoid accumulation and its contribution to flower coloration of Osmanthus fragrans. Front Plant Sci. 2018;9:1499.
Article
PubMed
PubMed Central
Google Scholar
Yamamoto T, Inui T, Tsuji T. The odor of Osmanthus fragrans attenuates food intake. Sci Rep. 2013;3:1518.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yang XL, Li HY, Yue YZ, Ding WJ, Xu C, Shi TT, et al. Transcriptomic analysis of the candidate genes related to aroma formation in Osmanthus fragrans. Molecules. 2018;23:1604.
Article
PubMed Central
CAS
Google Scholar
Han Y, Wang H, Wang X, Li K, Dong M, Li Y, et al. Mechanism of floral scent production in Osmanthus fragrans and the production and regulation of its key floral constituents, β-ionone and linalool. Hortic Res. 2019;6:106.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mao S, Wang K, Lei Y, Yao S, Lu B, Huang W. Antioxidant synergistic effects of Osmanthus fragrans flowers with green tea and their major contributed antioxidant compounds. Sci Rep. 2017;7:46501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhou F, Zhao Y, Li M, Xu T, Zhang L, Lu B, et al. Degradation of phenylethanoid glycosides in Osmanthus fragrans Lour flowers and its effect on anti-hypoxia activity. Sci Rep. 2017;7:10068.
Article
PubMed
PubMed Central
CAS
Google Scholar
He Y, Yuan W, Dong M, Han Y, Shang F. The first genetic map in sweet Osmanthus (Osmanthus fragrans Lour) using specific locus amplified fragment sequencing. Front Plant Sci. 2017;8:1621.
Article
PubMed
PubMed Central
Google Scholar
Yang X, Yue Y, Li H, Ding W, Chen G, Shi T, Chen J, Park MS, Chen F, Wang L. The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans. Hortic Res. 2018;5:72.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, et al. Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol. 2006;57:405–30.
Article
CAS
PubMed
Google Scholar
Buer CS, Muday GK. The transparent testa4 mutation prevents flavonoid synthesis and alters auxin transport and the response of Arabidopsis roots to gravity and light. Plant Cell. 2004;16:1191–205.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen GL, Chen SG, Xie YQ, Chen F, Zhao YY, Luo CX, et al. Total phenolic, flavonoid and antioxidant activity of 23 edible flowers subjected to in vitro digestion. J Funct Foods. 2015;17:243–59.
Article
CAS
Google Scholar
Wang Y, Fu J, Zhang C, Zhao H. HPLC-DAD-ESI-MS analysis of flavonoids from leaves of different cultivars of sweet Osmanthus. Molecules. 2016;21:1224.
Article
PubMed Central
CAS
Google Scholar
Zheng C, Ma JQ, Chen JD, Ma CL, Chen W, Yao MZ, et al. Gene Coexpression networks reveal key drivers of flavonoid variation in eleven tea cultivars (Camellia sinensis). J Agric Food Chem. 2019;67:9967–78.
Article
PubMed
Google Scholar
Gou JY, Felippes FF, Liu CJ, Weigel D, Wang JW. Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell. 2011;23:1512–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui LG, Shan JX, Shi M, Gao JP, Lin HX. The miR156- SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J. 2014;80:1108–17.
Article
CAS
PubMed
Google Scholar
Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK. MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. Plant Physiol. 2016;171:944–59.
CAS
PubMed
PubMed Central
Google Scholar
Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S. Identification of miRNAs involved in pear fruit development and quality. BMC Genomics. 2014;3:953.
Article
CAS
Google Scholar
Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, et al. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J. 2007;50:660–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chi X, Yang Q, Chen X, Wang J, Pan L, Chen M, et al. Identification and characterization of microRNAs from peanut (Arachis hypogaea L) by high-throughput sequencing. PLoS One. 2011;6:e27530.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xia H, Zhang L, Wu G, Fu C, Long Y, Xiang J, et al. Genome-wide identification and characterization of MicroRNAs and target genes in Lonicera japonica. PLoS One. 2016;11:e0164140.
Article
PubMed
PubMed Central
CAS
Google Scholar
An FM, Hsiao SR, Chan MT. Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in phalaenopsis orchid. PLoS One. 2011;6:e18937.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ben-Nissan G, Weiss D. Developmental and hormonal regulation of a Triosephosphate Isomerase gene in Petunia corollas. J Plant Physiol. 1995;147:58–62.
Article
CAS
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu HJ, Ma YK, Chen T, Wang M, Wang XJ. PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Res. 2012;40(Web Server issue):W22–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolle C. The role of GRAS proteins in plant signal transduction and development. Planta. 2004;218:683–92.
Article
CAS
PubMed
Google Scholar
Bonnet E, Wuyts J, Rouze P, Van de Peer Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics. 2004;20:2911–7.
Article
CAS
PubMed
Google Scholar
Gupta OP, Karkute SG, Banerjee S, Meena NL, Dahuja A. Contemporary understanding of miRNA-based regulation of secondary metabolites biosynthesis in plants. Front Plant Sci. 2017;8:374.
PubMed
PubMed Central
Google Scholar
Guo AY, Zhu QH, Gu X, Ge S, Yang J, Luo J. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene. 2008;418:1–8.
Article
CAS
PubMed
Google Scholar
Achard P, Herr A, Baulcombe DC, Harberd NP. Modulation of floral development by a gibberellin-regulated microRNA. Development. 2004;131:3357–65.
Article
CAS
PubMed
Google Scholar
Zhang Y, Wang L. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol. 2005;5:1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hunt M, Banerjee S, Surana P, Liu M, Fuerst G, Mathioni S, Meyers BC, Nettleton D, Wise RP. Small RNA discovery in the interaction between barley and the powdery mildew pathogen. BMC Genomics. 2019;20:610.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lindgreen S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res Notes. 2012;5:337.
Article
PubMed
PubMed Central
Google Scholar
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713–4.
Article
CAS
PubMed
Google Scholar
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013;41(Database issue):D226–32 2013.
Article
CAS
PubMed
Google Scholar
Velayudha Vimala Kumar K, Srikakulam N, Padbhanabhan P, Pandi G. Deciphering microRNAs and Their Associated Hairpin Precursors in a Non-Model Plant, Abelmoschus esculentus. Noncoding RNA. 2017;3:19.
PubMed Central
Google Scholar
Thakur V, Wanchana S, Xu M, Bruskiewich R, Quick WP, Mosig A, Zhu XG. Characterization of statistical features for plant microRNA prediction. BMC Genomics. 2011;12:108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Feng Z, Wang X, Wang X, Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics. 2010;26:136–8.
Article
PubMed
CAS
Google Scholar
Dewanto V, Wu XZ, Adom KK, Liu RH. Thermal processing enhances the nutritional value of tomatoes by increasing total antioxidant activity. J Agric Food Chem. 2002;50:3010–4.
Article
CAS
PubMed
Google Scholar