TY - JOUR AU - Myers, S. S. AU - Smith, M. R. AU - Guth, S. AU - Golden, C. D. AU - Vaitla, B. AU - Mueller, N. D. AU - Dangour, A. D. AU - Huybers, P. PY - 2017 DA - 2017// TI - Climate change and global food systems: potential impacts on food security and undernutrition JO - Annu Rev Public Health VL - 38 UR - https://doi.org/10.1146/annurev-publhealth-031816-044356 DO - 10.1146/annurev-publhealth-031816-044356 ID - Myers2017 ER - TY - STD TI - Sillmann, Kharin, V, V Zwiers, F. W, Bronaugh, Zhang: Climate extremes indices in the CMIP5 multimodel ensemble: Part 2.;Future climate projections. J Geophys Res Atmos 2013, 118(6):2473–2493. ID - ref2 ER - TY - JOUR AU - Munns, R. AU - Gilliham, M. PY - 2015 DA - 2015// TI - Salinity tolerance of crops - what is the cost? JO - New Phytol VL - 208 UR - https://doi.org/10.1111/nph.13519 DO - 10.1111/nph.13519 ID - Munns2015 ER - TY - CHAP AU - Al, J. E. PY - 2007 DA - 2007// TI - Paasche: IPCC [Intergovernmental Panel on Climate Change] . Climate Change 2007 BT - The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the IPCC PB - United Kingdom Cambridge University Press CY - Cambridge ID - Al2007 ER - TY - JOUR AU - Dai, A. PY - 2013 DA - 2013// TI - Increasing drought under global warming in observations and models JO - Nat Clim Chang VL - 3 UR - https://doi.org/10.1038/nclimate1633 DO - 10.1038/nclimate1633 ID - Dai2013 ER - TY - JOUR AU - Bruce, W. B. AU - Edmeades, G. O. AU - Barker, T. C. PY - 2002 DA - 2002// TI - Molecular and physiological approaches to maize improvement for drought tolerance JO - J Exp Bot VL - 53 UR - https://doi.org/10.1093/jexbot/53.366.13 DO - 10.1093/jexbot/53.366.13 ID - Bruce2002 ER - TY - JOUR AU - Nakashima, K. AU - Ito, Y. AU - Yamaguchi-Shinozaki, K. PY - 2009 DA - 2009// TI - Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses JO - Plant Physiol VL - 149 UR - https://doi.org/10.1104/pp.108.129791 DO - 10.1104/pp.108.129791 ID - Nakashima2009 ER - TY - JOUR AU - Pauli, A. AU - Rinn, J. L. AU - Schier, A. F. PY - 2011 DA - 2011// TI - Non-coding RNAs as regulators of embryogenesis JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg2904 DO - 10.1038/nrg2904 ID - Pauli2011 ER - TY - JOUR AU - Longfei, S. AU - Zhangli, H. PY - 2010 DA - 2010// TI - Small silencing RNAs in Chlamydomonas reinhardtii JO - Minerva Biotecnologica VL - 22 ID - Longfei2010 ER - TY - JOUR AU - Chekanova, J. A. PY - 2015 DA - 2015// TI - Long non-coding RNAs and their functions in plants JO - Curr Opin Plant Biol VL - 27 UR - https://doi.org/10.1016/j.pbi.2015.08.003 DO - 10.1016/j.pbi.2015.08.003 ID - Chekanova2015 ER - TY - JOUR AU - Liu, J. AU - Jung, C. AU - Xu, J. AU - Wang, H. AU - Deng, S. AU - Bernad, L. AU - Arenas-Huertero, C. AU - Chua, N. H. PY - 2012 DA - 2012// TI - Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis JO - Plant Cell VL - 24 UR - https://doi.org/10.1105/tpc.112.102855 DO - 10.1105/tpc.112.102855 ID - Liu2012 ER - TY - JOUR AU - Yamada, K. AU - Lim, J. AU - Dale, J. M. AU - Chen, H. AU - Shinn, P. AU - Palm, C. J. AU - Southwick, A. M. AU - Wu, H. C. AU - Kim, C. AU - Nguyen, M. PY - 2003 DA - 2003// TI - Empirical analysis of transcriptional activity in the Arabidopsis genome JO - Science (New York, NY) VL - 302 UR - https://doi.org/10.1126/science.1088305 DO - 10.1126/science.1088305 ID - Yamada2003 ER - TY - JOUR AU - Wang, X. J. AU - Gaasterland, T. AU - Chua, N. H. PY - 2005 DA - 2005// TI - Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana JO - Genome Biol VL - 6 UR - https://doi.org/10.1186/gb-2005-6-4-r30 DO - 10.1186/gb-2005-6-4-r30 ID - Wang2005 ER - TY - JOUR AU - Heo, J. B. AU - Sung, S. PY - 2011 DA - 2011// TI - Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA JO - Science (New York, NY) VL - 331 UR - https://doi.org/10.1126/science.1197349 DO - 10.1126/science.1197349 ID - Heo2011 ER - TY - JOUR AU - Campalans, A. AU - Kondorosi, A. AU - Crespi, M. PY - 2004 DA - 2004// TI - Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.019406 DO - 10.1105/tpc.019406 ID - Campalans2004 ER - TY - JOUR AU - Wang, Y. AU - Fan, X. AU - Lin, F. AU - He, G. AU - Terzaghi, W. AU - Zhu, D. AU - Deng, X. W. PY - 2014 DA - 2014// TI - Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1409457111 DO - 10.1073/pnas.1409457111 ID - Wang2014 ER - TY - JOUR AU - Zhang, Y. C. AU - Liao, J. Y. AU - Li, Z. Y. AU - Yu, Y. AU - Zhang, J. P. AU - Li, Q. F. AU - Qu, L. H. AU - Shu, W. S. AU - Chen, Y. Q. PY - 2014 DA - 2014// TI - Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0512-1 DO - 10.1186/s13059-014-0512-1 ID - Zhang2014 ER - TY - STD TI - Deng F, Zhang X, Wang W, Yuan R, Shen F: Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress 2018, 18(1):23. ID - ref18 ER - TY - JOUR AU - Li, S. AU - Yu, X. AU - Lei, N. AU - Cheng, Z. AU - Zhao, P. AU - He, Y. AU - Wang, W. AU - Peng, M. PY - 2017 DA - 2017// TI - Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep45981 DO - 10.1038/srep45981 ID - Li2017 ER - TY - JOUR AU - Kornienko, A. E. AU - Guenzl, P. M. AU - Barlow, D. P. AU - Pauler, F. M. PY - 2013 DA - 2013// TI - Gene regulation by the act of long non-coding RNA transcription JO - BMC Biol VL - 11 UR - https://doi.org/10.1186/1741-7007-11-59 DO - 10.1186/1741-7007-11-59 ID - Kornienko2013 ER - TY - JOUR AU - Ponting, C. P. AU - Oliver, P. L. AU - Reik, W. PY - 2009 DA - 2009// TI - Evolution and functions of long noncoding RNAs JO - Cell VL - 136 UR - https://doi.org/10.1016/j.cell.2009.02.006 DO - 10.1016/j.cell.2009.02.006 ID - Ponting2009 ER - TY - JOUR AU - Wierzbicki, A. T. PY - 2012 DA - 2012// TI - The role of long non-coding RNA in transcriptional gene silencing JO - Curr Opin Plant Biol VL - 15 UR - https://doi.org/10.1016/j.pbi.2012.08.008 DO - 10.1016/j.pbi.2012.08.008 ID - Wierzbicki2012 ER - TY - JOUR AU - Lucia, F. AU - Dean, C. PY - 2011 DA - 2011// TI - Long non-coding RNAs and chromatin regulation JO - Curr Opin Plant Biol VL - 14 UR - https://doi.org/10.1016/j.pbi.2010.11.006 DO - 10.1016/j.pbi.2010.11.006 ID - Lucia2011 ER - TY - JOUR AU - Swiezewski, S. AU - Liu, F. AU - Magusin, A. AU - Dean, C. PY - 2009 DA - 2009// TI - Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08618 DO - 10.1038/nature08618 ID - Swiezewski2009 ER - TY - JOUR AU - Franco-Zorrilla, J. M. AU - Valli, A. AU - Todesco, M. AU - Mateos, I. AU - Puga, M. I. AU - Rubio-Somoza, I. AU - Leyva, A. AU - Weigel, D. AU - Garcia, J. A. AU - Paz-Ares, J. PY - 2007 DA - 2007// TI - Target mimicry provides a new mechanism for regulation of microRNA activity JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng2079 DO - 10.1038/ng2079 ID - Franco-Zorrilla2007 ER - TY - JOUR AU - Shin, H. AU - Shin, H. S. AU - Chen, R. AU - Harrison, M. J. PY - 2006 DA - 2006// TI - Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation JO - Plant J VL - 45 UR - https://doi.org/10.1111/j.1365-313X.2005.02629.x DO - 10.1111/j.1365-313X.2005.02629.x ID - Shin2006 ER - TY - JOUR AU - Marker, C. AU - Zemann, A. AU - Terhorst, T. AU - Kiefmann, M. AU - Kastenmayer, J. P. AU - Green, P. AU - Bachellerie, J. P. AU - Brosius, J. AU - Huttenhofer, A. PY - 2002 DA - 2002// TI - Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana JO - Current biology : CB VL - 12 UR - https://doi.org/10.1016/S0960-9822(02)01304-0 DO - 10.1016/S0960-9822(02)01304-0 ID - Marker2002 ER - TY - STD TI - Paytuvi Gallart A, Hermoso Pulido A: GREENC: a Wiki-based database of plant lncRNAs. 2016, 44(D1):D1161–1166. ID - ref28 ER - TY - STD TI - Yang J. Effects of grazing systems on the reproductive feature of key plant population in Stipa breviflora steppe. J Arid Land Res Environ. 2001. ID - ref29 ER - TY - JOUR AU - Zhang, J. AU - John, U. P. AU - Wang, Y. AU - Li, X. AU - Gunawardana, D. AU - Polotnianka, R. M. AU - Spangenberg, G. C. AU - Nan, Z. PY - 2011 DA - 2011// TI - Targeted mining of drought stress-responsive genes from EST resources in Cleistogenes songorica JO - J Plant Physiol VL - 168 UR - https://doi.org/10.1016/j.jplph.2011.04.005 DO - 10.1016/j.jplph.2011.04.005 ID - Zhang2011 ER - TY - JOUR AU - Zhang, J. AU - Zhen, D. AU - Jahufer, Z. AU - An, S. J. AU - Wang, Y. R. PY - 2014 DA - 2014// TI - Stress-inducible expression of a Cleistogenes songorica ALDH gene enhanced drought tolerance in transgenic Arabidopsis thaliana JO - Plant Omics VL - 7 ID - Zhang2014 ER - TY - STD TI - Duan Z, Zhang D, Zhang J, Di H, Wu F, Hu X, Meng X, Luo K, Zhang J, Wang Y: Co-transforming bar and CsALDH Genes Enhanced Resistance to Herbicide and Drought and Salt Stress in Transgenic Alfalfa (Medicago sativa L.). Front Plant Sci 2015, 6:1115. ID - ref32 ER - TY - JOUR AU - Zhang, J. AU - Duan, Z. AU - Zhang, D. AU - Zhang, J. AU - Di, H. AU - Wu, F. AU - Wang, Y. PY - 2016 DA - 2016// TI - Co-transforming bar and CsLEA enhanced tolerance to drought and salt stress in transgenic alfalfa (Medicago sativa L.) JO - Biochem Biophys Res Commun VL - 472 UR - https://doi.org/10.1016/j.bbrc.2016.02.067 DO - 10.1016/j.bbrc.2016.02.067 ID - Zhang2016 ER - TY - JOUR AU - Zhang, J. AU - Kong, L. AU - Liu, Z. AU - Jahufer, Z. AU - Duan, Z. AU - Huo, Y. AU - Di, H. AU - Wang, Y. PY - 2015 DA - 2015// TI - Stress-induced expression in Arabidopsis with a Dehydrin LEA protein from Cleistogenes songorica, a xerophytic desert grass JO - Plant Omics VL - 8 ID - Zhang2015 ER - TY - JOUR AU - Jianwei, L. AU - Wei, M. AU - Pan, Z. AU - Junyi, W. AU - Bin, G. AU - Jichun, Y. AU - Qinghua, C. PY - 2015 DA - 2015// TI - LncTar: a tool for predicting the RNA targets of long noncoding RNAs JO - Brief Bioinform VL - 16 UR - https://doi.org/10.1093/bib/bbu048 DO - 10.1093/bib/bbu048 ID - Jianwei2015 ER - TY - JOUR AU - Ray, S. AU - Dansana, P. K. AU - Giri, J. AU - Deveshwar, P. AU - Arora, R. AU - Agarwal, P. AU - Khurana, J. P. AU - Kapoor, S. AU - Tyagi, A. K. PY - 2011 DA - 2011// TI - Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice JO - Funct Integr Genomics VL - 11 UR - https://doi.org/10.1007/s10142-010-0187-y DO - 10.1007/s10142-010-0187-y ID - Ray2011 ER - TY - JOUR AU - Zhang, L. AU - Yu, S. AU - Zuo, K. AU - Luo, L. AU - Tang, K. PY - 2012 DA - 2012// TI - Identification of gene modules associated with drought response in rice by network-based analysis JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0033748 DO - 10.1371/journal.pone.0033748 ID - Zhang2012 ER - TY - JOUR AU - Wang, T. Z. AU - Liu, M. AU - Zhao, M. G. AU - Chen, R. AU - Zhang, W. H. PY - 2015 DA - 2015// TI - Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing JO - BMC Plant Biol VL - 15 UR - https://doi.org/10.1186/s12870-015-0530-5 DO - 10.1186/s12870-015-0530-5 ID - Wang2015 ER - TY - JOUR AU - Di, C. AU - Yuan, J. AU - Wu, Y. AU - Li, J. AU - Lin, H. AU - Hu, L. AU - Zhang, T. AU - Qi, Y. AU - Gerstein, M. B. AU - Guo, Y. PY - 2014 DA - 2014// TI - Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features JO - Plant J VL - 80 UR - https://doi.org/10.1111/tpj.12679 DO - 10.1111/tpj.12679 ID - Di2014 ER - TY - JOUR AU - Wu, F. AU - Zhang, D. AU - Muvunyi, B. P. AU - Yan, Q. AU - Zhang, Y. AU - Yan, Z. AU - Cao, M. AU - Wang, Y. AU - Zhang, J. PY - 2018 DA - 2018// TI - Analysis of microRNA reveals cleistogamous and chasmogamous floret divergence in dimorphic plant JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-24477-x DO - 10.1038/s41598-018-24477-x ID - Wu2018 ER - TY - JOUR AU - Li, L. AU - Eichten, S. R. AU - Shimizu, R. AU - Petsch, K. AU - Yeh, C. T. AU - Wu, W. AU - Chettoor, A. M. AU - Givan, S. A. AU - Cole, R. A. AU - Fowler, J. E. PY - 2014 DA - 2014// TI - Genome-wide discovery and characterization of maize long non-coding RNAs JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-2-r40 DO - 10.1186/gb-2014-15-2-r40 ID - Li2014 ER - TY - JOUR AU - Wang, D. AU - Pan, Y. AU - Zhao, X. AU - Zhu, L. AU - Fu, B. AU - Li, Z. PY - 2011 DA - 2011// TI - Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-149 DO - 10.1186/1471-2164-12-149 ID - Wang2011 ER - TY - JOUR AU - Li, H. AU - Wang, Y. AU - Chen, M. AU - Xiao, P. AU - Hu, C. AU - Zeng, Z. AU - Wang, C. AU - Wang, J. AU - Hu, Z. PY - 2016 DA - 2016// TI - Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep34109 DO - 10.1038/srep34109 ID - Li2016 ER - TY - JOUR AU - Dixon, R. A. AU - Paiva, N. L. PY - 1995 DA - 1995// TI - Stress-induced Phenylpropanoid metabolism JO - Plant Cell VL - 7 UR - https://doi.org/10.1105/tpc.7.7.1085 DO - 10.1105/tpc.7.7.1085 ID - Dixon1995 ER - TY - JOUR AU - Bari, R. AU - Jones, J. D. PY - 2009 DA - 2009// TI - Role of plant hormones in plant defence responses JO - Plant Mol Biol VL - 69 UR - https://doi.org/10.1007/s11103-008-9435-0 DO - 10.1007/s11103-008-9435-0 ID - Bari2009 ER - TY - JOUR AU - Carretero-Paulet, L. AU - Galstyan, A. AU - Roig-Villanova, I. AU - Martínez-García, J. F. AU - Bilbao-Castro, J. R. AU - Robertson, D. L. PY - 2010 DA - 2010// TI - Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, Rice, Moss, and algae JO - Plant Physiol VL - 153 UR - https://doi.org/10.1104/pp.110.153593 DO - 10.1104/pp.110.153593 ID - Carretero-Paulet2010 ER - TY - JOUR AU - Wang, Y. AU - Fan, X. AU - Lin, F. AU - He, G. AU - Terzaghi, W. AU - Zhu, D. AU - Deng, X. W. PY - 2014 DA - 2014// TI - Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1409457111 DO - 10.1073/pnas.1409457111 ID - Wang2014 ER - TY - JOUR AU - Hu, H. AU - Dai, M. AU - Yao, J. AU - Xiao, B. AU - Li, X. AU - Zhang, Q. AU - Xiong, L. PY - 2006 DA - 2006// TI - Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0604882103 DO - 10.1073/pnas.0604882103 ID - Hu2006 ER - TY - JOUR AU - Hu, H. AU - You, J. AU - Fang, Y. AU - Zhu, X. AU - Qi, Z. AU - Xiong, L. PY - 2008 DA - 2008// TI - Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice JO - Plant Mol Biol VL - 67 UR - https://doi.org/10.1007/s11103-008-9309-5 DO - 10.1007/s11103-008-9309-5 ID - Hu2008 ER - TY - JOUR AU - Hong, Y. AU - Zhang, H. AU - Huang, L. AU - Li, D. AU - Song, F. PY - 2016 DA - 2016// TI - Overexpression of a stress-responsive NAC transcription factor gene ONAC022 improves drought and salt tolerance in Rice JO - Front Plant Sci VL - 7 UR - https://doi.org/10.3389/fpls.2016.00004 DO - 10.3389/fpls.2016.00004 ID - Hong2016 ER - TY - JOUR AU - Lee, D. K. AU - Chung, P. J. AU - Jeong, J. S. AU - Jang, G. AU - Bang, S. W. AU - Jung, H. AU - Kim, Y. S. AU - Ha, S. H. AU - Choi, Y. D. AU - Kim, J. K. PY - 2017 DA - 2017// TI - The rice OsNAC6 transcription factor orchestrates multiple molecular mechanisms involving root structural adaptions and nicotianamine biosynthesis for drought tolerance JO - Plant Biotechnol J VL - 15 UR - https://doi.org/10.1111/pbi.12673 DO - 10.1111/pbi.12673 ID - Lee2017 ER - TY - JOUR AU - Nakashima, K. AU - Tran, L. S. AU - Nguyen, D. AU - Fujita, M. AU - Maruyama, K. AU - Todaka, D. AU - Ito, Y. AU - Hayashi, N. AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. PY - 2007 DA - 2007// TI - Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice JO - Plant J VL - 51 UR - https://doi.org/10.1111/j.1365-313X.2007.03168.x DO - 10.1111/j.1365-313X.2007.03168.x ID - Nakashima2007 ER - TY - JOUR AU - Jeong, J. S. AU - Kim, Y. S. AU - Baek, K. H. AU - Jung, H. AU - Ha, S. H. AU - Choi, Y. AU - Kim, M. AU - Reuzeau, C. AU - Kim, J. K. PY - 2010 DA - 2010// TI - Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions JO - Plant Physiol VL - 153 UR - https://doi.org/10.1104/pp.110.154773 DO - 10.1104/pp.110.154773 ID - Jeong2010 ER - TY - STD TI - Tang N, Ma S, Zong W, Yang N, Lv Y, Yan C, Guo Z, Li J, Li X, Xiang Y, et al. MODD mediates deactivation and degradation of OsbZIP46 to negatively regulate ABA signaling and drought resistance in rice. Plant Cell. 2016. ID - ref54 ER - TY - JOUR AU - Yoon, S. AU - Lee, D. -. K. AU - Yu, I. J. AU - Kim, Y. S. AU - Choi, Y. D. AU - Kim, J. -. K. PY - 2017 DA - 2017// TI - Overexpression of the OsbZIP66 transcription factor enhances drought tolerance of rice plants JO - Plant Biotech Reports VL - 11 UR - https://doi.org/10.1007/s11816-017-0430-2 DO - 10.1007/s11816-017-0430-2 ID - Yoon2017 ER - TY - JOUR AU - Qi, X. AU - Xie, S. AU - Liu, Y. AU - Yi, F. AU - Yu, J. PY - 2013 DA - 2013// TI - Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing JO - Plant Mol Biol VL - 83 UR - https://doi.org/10.1007/s11103-013-0104-6 DO - 10.1007/s11103-013-0104-6 ID - Qi2013 ER - TY - JOUR AU - Dugas, D. V. AU - Monaco, M. K. AU - Olsen, A. AU - Klein, R. R. AU - Kumari, S. AU - Ware, D. AU - Klein, P. E. PY - 2011 DA - 2011// TI - Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-514 DO - 10.1186/1471-2164-12-514 ID - Dugas2011 ER - TY - JOUR AU - Jain, M. AU - Tyagi, A. K. AU - Khurana, J. P. PY - 2008 DA - 2008// TI - Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice JO - FEBS J VL - 275 UR - https://doi.org/10.1111/j.1742-4658.2008.06424.x DO - 10.1111/j.1742-4658.2008.06424.x ID - Jain2008 ER - TY - JOUR AU - Bhattacharjee, A. AU - Sharma, R. AU - Jain, M. PY - 2017 DA - 2017// TI - Over-expression of OsHOX24 confers enhanced susceptibility to abiotic stresses in transgenic Rice via modulating stress-responsive gene expression JO - Front Plant Sci VL - 8 UR - https://doi.org/10.3389/fpls.2017.00628 DO - 10.3389/fpls.2017.00628 ID - Bhattacharjee2017 ER - TY - JOUR AU - Zhang, S. AU - Haider, I. AU - Kohlen, W. AU - Jiang, L. AU - Bouwmeester, H. AU - Meijer, A. H. AU - Schluepmann, H. AU - Liu, C. M. AU - Ouwerkerk, P. B. PY - 2012 DA - 2012// TI - Function of the HD-zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice JO - Plant Mol Biol VL - 80 UR - https://doi.org/10.1007/s11103-012-9967-1 DO - 10.1007/s11103-012-9967-1 ID - Zhang2012 ER - TY - JOUR AU - Watanabe, S. AU - Kojima, K. AU - Ide, Y. AU - Sasaki, S. PY - 2000 DA - 2000// TI - Effects of saline and osmotic stress on proline and sugar accumulation in Populus euphratica in vitro JO - Plant Cell Tiss Org Cult VL - 63 UR - https://doi.org/10.1023/A:1010619503680 DO - 10.1023/A:1010619503680 ID - Watanabe2000 ER - TY - STD TI - Singh D, Laxmi A: Transcriptional regulation of drought response: a tortuous network of transcriptional factors. Front Plant Sci 2015, 6(895). ID - ref62 ER - TY - JOUR AU - Kang, J. AU - Hwang, J. U. AU - Lee, M. AU - Kim, Y. Y. AU - Assmann, S. M. AU - Martinoia, E. AU - Lee, Y. PY - 2010 DA - 2010// TI - PDR-type ABC transporter mediates cellular uptake of the phytohormone abscisic acid JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0909222107 DO - 10.1073/pnas.0909222107 ID - Kang2010 ER - TY - JOUR AU - Axtell, M. J. PY - 2013 DA - 2013// TI - Classification and comparison of small RNAs from plants JO - Annu Rev Plant Biol VL - 64 UR - https://doi.org/10.1146/annurev-arplant-050312-120043 DO - 10.1146/annurev-arplant-050312-120043 ID - Axtell2013 ER - TY - JOUR AU - Fan, C. AU - Hao, Z. AU - Yan, J. AU - Li, G. PY - 2015 DA - 2015// TI - Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-2024-0 DO - 10.1186/s12864-015-2024-0 ID - Fan2015 ER - TY - JOUR AU - Fang, Y. AU - Xie, K. AU - Xiong, L. PY - 2014 DA - 2014// TI - Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice JO - J Exp Bot VL - 65 UR - https://doi.org/10.1093/jxb/eru072 DO - 10.1093/jxb/eru072 ID - Fang2014 ER - TY - JOUR AU - Si-Ammour, A. AU - Vazquez, F. PY - 2011 DA - 2011// TI - miR393 and secondary siRNAs regulate expression of the TIR1/AFB2 auxin receptor clade and auxin-related development of Arabidopsis leaves JO - Plant Physiol VL - 157 UR - https://doi.org/10.1104/pp.111.180083 DO - 10.1104/pp.111.180083 ID - Si-Ammour2011 ER - TY - JOUR AU - Mittler, R. AU - Vanderauwera, S. AU - Gollery, M. AU - Van, B. F. PY - 2004 DA - 2004// TI - Reactive oxygen gene network of plants JO - Trends Plant Sci VL - 9 UR - https://doi.org/10.1016/j.tplants.2004.08.009 DO - 10.1016/j.tplants.2004.08.009 ID - Mittler2004 ER - TY - JOUR AU - Yu, Y. AU - Li, Q. F. AU - Zhang, J. P. AU - Zhang, F. AU - Zhou, Y. F. AU - Feng, Y. Z. AU - Chen, Y. Q. AU - Zhang, Y. C. PY - 2017 DA - 2017// TI - Laccase-13 regulates seed setting rate by affecting hydrogen peroxide dynamics and mitochondrial integrity in Rice JO - Front Plant Sci VL - 8 UR - https://doi.org/10.3389/fpls.2017.01324 DO - 10.3389/fpls.2017.01324 ID - Yu2017 ER - TY - STD TI - Berthet S, Demont-Caulet N, Pollet B, Bidzinski P, Cã©Zard L, Le BP, Borrega N, Hervã© J, Blondet E, Balzergue S: disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of Arabidopsis thaliana stems. Plant Cell 2011, 23(3):1124–1137. ID - ref70 ER - TY - STD TI - Kim D, Langmead B, Salzberg SL: HISAT: a fast spliced aligner with low memory requirements 2015, 12(4):357–360. ID - ref71 ER - TY - STD TI - Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads 2015, 33(3):290–295. ID - ref72 ER - TY - JOUR AU - Lv, J. AU - Huang, Z. AU - Liu, H. AU - Liu, H. AU - Cui, W. AU - Li, B. AU - He, H. AU - Guo, J. AU - Liu, Q. AU - Zhang, Y. PY - 2014 DA - 2014// TI - Identification and characterization of long intergenic non-coding RNAs related to mouse liver development JO - Mol Genet Genomics : MGG VL - 289 UR - https://doi.org/10.1007/s00438-014-0882-9 DO - 10.1007/s00438-014-0882-9 ID - Lv2014 ER - TY - JOUR AU - Kelley, D. AU - Rinn, J. PY - 2012 DA - 2012// TI - Transposable elements reveal a stem cell-specific class of long noncoding RNAs JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-11-r107 DO - 10.1186/gb-2012-13-11-r107 ID - Kelley2012 ER - TY - JOUR AU - Wang, L. AU - Park, H. J. AU - Dasari, S. AU - Wang, S. AU - Kocher, J. P. AU - Li, W. PY - 2013 DA - 2013// TI - CPAT: coding-potential assessment tool using an alignment-free logistic regression model JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt006 DO - 10.1093/nar/gkt006 ID - Wang2013 ER - TY - JOUR AU - Sun, L. AU - Luo, H. AU - Bu, D. AU - Zhao, G. AU - Yu, K. AU - Zhang, C. AU - Liu, Y. AU - Chen, R. AU - Zhao, Y. PY - 2013 DA - 2013// TI - Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt646 DO - 10.1093/nar/gkt646 ID - Sun2013 ER - TY - STD TI - Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G: CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic acids research 2007, 35(Web Server issue):W345–349. ID - ref77 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. AU - Heger, A. AU - Hetherington, K. AU - Holm, L. AU - Mistry, J. PY - 2014 DA - 2014// TI - Pfam: the protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 ER - TY - STD TI - Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. 2016;11(9):1650–67. ID - ref79 ER - TY - JOUR AU - Young, M. D. AU - Wakefield, M. J. AU - Smyth, G. K. AU - Oshlack, A. PY - 2010 DA - 2010// TI - Gene ontology analysis for RNA-seq: accounting for selection bias JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-2-r14 DO - 10.1186/gb-2010-11-2-r14 ID - Young2010 ER - TY - JOUR AU - Mao, X. AU - Cai, T. AU - Olyarchuk, J. G. AU - Wei, L. PY - 2005 DA - 2005// TI - Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti430 DO - 10.1093/bioinformatics/bti430 ID - Mao2005 ER - TY - JOUR AU - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - STD TI - Dai X, Zhuang Z. Zhao PX: psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018. ID - ref83 ER -