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Found 2 results
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2016
Y. Shen, Liu, Y. H., Zhang, X. J., Sha, Q., Chen, Z. D., Shen, Y., Liu, Y. H., Zhang, X. J., Sha, Q., and Chen, Z. D., Gynophore miRNA analysis at different developmental stages in Arachis duranensis, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSResearch supported by the Self-Directed Innovation Fund of Agricultural Science and Technology in Jiangsu Province, China (grant #CX(13)5006). We thank Gene Pioneer Biotechnologies for their help with the bioinformatic analyses. REFERENCESAllen E, Xie Z, Gustafson AM, Carrington JC, et al (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221. http://dx.doi.org/10.1016/j.cell.2005.04.004 Chen X, Zhu W, Azam S, Li H, et al (2013). Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol. J. 11: 115-127. http://dx.doi.org/10.1111/pbi.12018 Chen X, Yang Q, Li H, Li H, et al (2016). Transcriptome-wide sequencing provides insights into geocarpy in peanut (Arachis hypogaea L.). Plant Biotechnol. J. 14: 1215-1224. http://dx.doi.org/10.1111/pbi.12487 Chen ZB, Wang ML, Barkley NA, Pittman RN, et al (2010). A simple allele-specific PCR assay for detecting FAD2 alleles in both A and B genomes of the cultivated peanut for high-oleate trait selection. Plant Mol. Biol. Rep. 28: 542-548. http://dx.doi.org/10.1007/s11105-010-0181-5 Chi X, Yang Q, Chen X, Wang J, et al (2011). Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One 6: e27530. http://dx.doi.org/10.1371/journal.pone.0027530 Deng X, Li Z, Zhang W, et al (2012). Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil. Food Microbiol. 30: 311-315. http://dx.doi.org/10.1016/j.fm.2011.11.001 Du Z, Zhou X, Ling Y, Zhang Z, et al (2010). agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38: W64-70. http://dx.doi.org/10.1093/nar/gkq310 Floyd SK, Bowman JL, et al (2004). Gene regulation: ancient microRNA target sequences in plants. Nature 428: 485-486. http://dx.doi.org/10.1038/428485a Griffiths-Jones S, et al (2006). miRBase: the microRNA sequence database. Methods Mol. Biol. 342: 129-138. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, et al (2005). Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124. http://dx.doi.org/10.1093/nar/gki081 Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, et al (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34: D140-D144. http://dx.doi.org/10.1093/nar/gkj112 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, et al (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res. 36: D154-D158. http://dx.doi.org/10.1093/nar/gkm952 Herr AJ, et al (2005). Pathways through the small RNA world of plants. FEBS Lett. 579: 5879-5888. http://dx.doi.org/10.1016/j.febslet.2005.08.040 Lee RC, Feinbaum RL, Ambros V, et al (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854. http://dx.doi.org/10.1016/0092-8674(93)90529-Y Li M, Zhao SZ, Zhao CZ, Zhang Y, et al. (2016). Cloning and characterization of SPL-family genes in the peanut (Arachis hypogaea L.). Genet. Mol. Res. 15: gmr.15017344. Mi S, Cai T, Hu Y, Chen Y, et al (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127. http://dx.doi.org/10.1016/j.cell.2008.02.034 Moctezuma E, et al (2003). The peanut gynophore: a developmental and physiological perspective. Can. J. Bot. 81: 183-190. http://dx.doi.org/10.1139/b03-024 Sunkar R, Jagadeeswaran G, et al (2008). In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 8: 37. http://dx.doi.org/10.1186/1471-2229-8-37 Sunkar R, Zhou X, Zheng Y, Zhang W, et al (2008). Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 8: 25. http://dx.doi.org/10.1186/1471-2229-8-25 Vazquez F, et al (2006). Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci. 11: 460-468. http://dx.doi.org/10.1016/j.tplants.2006.07.006 Wang C, Li C, Hou L, Liu X, et al (2013). Cloning and expression analysis of Gibberellin 2-Oxidase gene from peanut (Arachis hypogaea L). Shandong Agric. Sci. 45: 14-18. Xia H, Zhao C, Hou L, Li A, et al (2013). Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness. BMC Genomics 14: 517. http://dx.doi.org/10.1186/1471-2164-14-517 Yao Y, Guo G, Ni Z, Sunkar R, et al (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 8: R96. http://dx.doi.org/10.1186/gb-2007-8-6-r96 Zhang B, Pan X, Cannon CH, Cobb GP, et al (2006). Conservation and divergence of plant microRNA genes. Plant J. 46: 243-259. http://dx.doi.org/10.1111/j.1365-313X.2006.02697.x Zhao CZ, Xia H, Frazier TP, Yao YY, et al (2010). Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol. 10: 3. http://dx.doi.org/10.1186/1471-2229-10-3 Zhao C, Zhao S, Hou L, Xia H, et al (2015). Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages. BMC Plant Biol. 15: 188. http://dx.doi.org/10.1186/s12870-015-0582-6 Zhu W, Zhang E, Li H, Chen X, et al (2013). Comparative proteomics analysis of developing peanut aerial and subterranean pods identifies pod swelling related proteins. J. Proteomics 91: 172-187. http://dx.doi.org/10.1016/j.jprot.2013.07.002 Zhu W, Chen X, Li H, Zhu F, et al (2014). Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut. Plant Mol. Biol. 85: 395-409. http://dx.doi.org/10.1007/s11103-014-0193-x Zuker M, et al (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. http://dx.doi.org/10.1093/nar/gkg595  
Y. Shen, Liu, Y. H., Zhang, X. J., Sha, Q., Chen, Z. D., Shen, Y., Liu, Y. H., Zhang, X. J., Sha, Q., and Chen, Z. D., Gynophore miRNA analysis at different developmental stages in Arachis duranensis, vol. 15, no. 4, p. -, 2016.
Conflicts of interestThe authors declare no conflict of interest.ACKNOWLEDGMENTSResearch supported by the Self-Directed Innovation Fund of Agricultural Science and Technology in Jiangsu Province, China (grant #CX(13)5006). We thank Gene Pioneer Biotechnologies for their help with the bioinformatic analyses. REFERENCESAllen E, Xie Z, Gustafson AM, Carrington JC, et al (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221. http://dx.doi.org/10.1016/j.cell.2005.04.004 Chen X, Zhu W, Azam S, Li H, et al (2013). Deep sequencing analysis of the transcriptomes of peanut aerial and subterranean young pods identifies candidate genes related to early embryo abortion. Plant Biotechnol. J. 11: 115-127. http://dx.doi.org/10.1111/pbi.12018 Chen X, Yang Q, Li H, Li H, et al (2016). Transcriptome-wide sequencing provides insights into geocarpy in peanut (Arachis hypogaea L.). Plant Biotechnol. J. 14: 1215-1224. http://dx.doi.org/10.1111/pbi.12487 Chen ZB, Wang ML, Barkley NA, Pittman RN, et al (2010). A simple allele-specific PCR assay for detecting FAD2 alleles in both A and B genomes of the cultivated peanut for high-oleate trait selection. Plant Mol. Biol. Rep. 28: 542-548. http://dx.doi.org/10.1007/s11105-010-0181-5 Chi X, Yang Q, Chen X, Wang J, et al (2011). Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by high-throughput sequencing. PLoS One 6: e27530. http://dx.doi.org/10.1371/journal.pone.0027530 Deng X, Li Z, Zhang W, et al (2012). Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil. Food Microbiol. 30: 311-315. http://dx.doi.org/10.1016/j.fm.2011.11.001 Du Z, Zhou X, Ling Y, Zhang Z, et al (2010). agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 38: W64-70. http://dx.doi.org/10.1093/nar/gkq310 Floyd SK, Bowman JL, et al (2004). Gene regulation: ancient microRNA target sequences in plants. Nature 428: 485-486. http://dx.doi.org/10.1038/428485a Griffiths-Jones S, et al (2006). miRBase: the microRNA sequence database. Methods Mol. Biol. 342: 129-138. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, et al (2005). Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124. http://dx.doi.org/10.1093/nar/gki081 Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, et al (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34: D140-D144. http://dx.doi.org/10.1093/nar/gkj112 Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, et al (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res. 36: D154-D158. http://dx.doi.org/10.1093/nar/gkm952 Herr AJ, et al (2005). Pathways through the small RNA world of plants. FEBS Lett. 579: 5879-5888. http://dx.doi.org/10.1016/j.febslet.2005.08.040 Lee RC, Feinbaum RL, Ambros V, et al (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854. http://dx.doi.org/10.1016/0092-8674(93)90529-Y Li M, Zhao SZ, Zhao CZ, Zhang Y, et al. (2016). Cloning and characterization of SPL-family genes in the peanut (Arachis hypogaea L.). Genet. Mol. Res. 15: gmr.15017344. Mi S, Cai T, Hu Y, Chen Y, et al (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116-127. http://dx.doi.org/10.1016/j.cell.2008.02.034 Moctezuma E, et al (2003). The peanut gynophore: a developmental and physiological perspective. Can. J. Bot. 81: 183-190. http://dx.doi.org/10.1139/b03-024 Sunkar R, Jagadeeswaran G, et al (2008). In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 8: 37. http://dx.doi.org/10.1186/1471-2229-8-37 Sunkar R, Zhou X, Zheng Y, Zhang W, et al (2008). Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 8: 25. http://dx.doi.org/10.1186/1471-2229-8-25 Vazquez F, et al (2006). Arabidopsis endogenous small RNAs: highways and byways. Trends Plant Sci. 11: 460-468. http://dx.doi.org/10.1016/j.tplants.2006.07.006 Wang C, Li C, Hou L, Liu X, et al (2013). Cloning and expression analysis of Gibberellin 2-Oxidase gene from peanut (Arachis hypogaea L). Shandong Agric. Sci. 45: 14-18. Xia H, Zhao C, Hou L, Li A, et al (2013). Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness. BMC Genomics 14: 517. http://dx.doi.org/10.1186/1471-2164-14-517 Yao Y, Guo G, Ni Z, Sunkar R, et al (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 8: R96. http://dx.doi.org/10.1186/gb-2007-8-6-r96 Zhang B, Pan X, Cannon CH, Cobb GP, et al (2006). Conservation and divergence of plant microRNA genes. Plant J. 46: 243-259. http://dx.doi.org/10.1111/j.1365-313X.2006.02697.x Zhao CZ, Xia H, Frazier TP, Yao YY, et al (2010). Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol. 10: 3. http://dx.doi.org/10.1186/1471-2229-10-3 Zhao C, Zhao S, Hou L, Xia H, et al (2015). Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages. BMC Plant Biol. 15: 188. http://dx.doi.org/10.1186/s12870-015-0582-6 Zhu W, Zhang E, Li H, Chen X, et al (2013). Comparative proteomics analysis of developing peanut aerial and subterranean pods identifies pod swelling related proteins. J. Proteomics 91: 172-187. http://dx.doi.org/10.1016/j.jprot.2013.07.002 Zhu W, Chen X, Li H, Zhu F, et al (2014). Comparative transcriptome analysis of aerial and subterranean pods development provides insights into seed abortion in peanut. Plant Mol. Biol. 85: 395-409. http://dx.doi.org/10.1007/s11103-014-0193-x Zuker M, et al (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. http://dx.doi.org/10.1093/nar/gkg595