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Linked References

1. E. Mazzucotelli, A. M. Mastrangelo, C. Crosatti, D. Guerra, A. M. Stanca, and L. Cattivelli, “Abiotic stress response in plants: when post-transcriptional and post-translational regulations control transcription,” Plant Science, vol. 174, no. 4, pp. 420–431, 2008. View at Publisher · View at Google Scholar · View at Scopus
2. K. Nakaminami, A. Matsui, K. Shinozaki, and M. Seki, “RNA regulation in plant abiotic stress responses,” Biochimica Et Biophysica Acta, vol. 1819, no. 2, pp. 149–153, 2012. View at Publisher · View at Google Scholar
3. D. L. Black, “Mechanisms of alternative pre-messenger RNA splicing,” Annual Review of Biochemistry, vol. 72, pp. 291–336, 2003. View at Publisher · View at Google Scholar · View at Scopus
4. A. S. N. Reddy, “Alternative splicing of pre-messenger RNAs in plants in the genomic era,” Annual Review of Plant Biology, vol. 58, pp. 267–294, 2007. View at Publisher · View at Google Scholar · View at Scopus
5. S. A. Filichkin, H. D. Priest, S. A. Givan et al., “Genome-wide mapping of alternative splicing in Arabidopsis thaliana,” Genome Research, vol. 20, no. 1, pp. 45–58, 2010. View at Publisher · View at Google Scholar · View at Scopus
6. Y. Marquez, J. W. Brown, C. Simpson, et al., “Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis,” Genome Resources, vol. 22, no. 6, pp. 1184–1195, 2012. View at Publisher · View at Google Scholar
7. K. Iida, M. Seki, T. Sakurai et al., “Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences,” Nucleic Acids Research, vol. 32, no. 17, pp. 5096–5103, 2004. View at Publisher · View at Google Scholar · View at Scopus
8. B. B. Wang and V. Brendel, “Genomewide comparative analysis of alternative splicing in plants,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 18, pp. 7175–7180, 2006. View at Publisher · View at Google Scholar · View at Scopus
9. G. S. Ali and A. S. N. Reddy, “Regulation of alternative splicing of pre-mRNAs by stresses,” Current Topics in Microbiology and Immunology, vol. 326, pp. 257–275, 2008. View at Publisher · View at Google Scholar · View at Scopus
10. A. M. Mastrangelo, D. Marone, G. Laidò, et al., “Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity,” Plant Science, vol. 185-186, pp. 40–49, 2012. View at Publisher · View at Google Scholar
11. X. Niu, D. Luo, S. Gao et al., “A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants,” Journal of Genetics and Genomics, vol. 37, no. 1, pp. 85–99, 2010. View at Publisher · View at Google Scholar · View at Scopus
12. S. A. Filichkin and T. C. Mockler, “Unproductive alternative splicing and nonsense mRNAs: a widespread phenomenon among plant circadian clock genes,” Biology Direct, vol. 7, no. 1, p. 20, 2012. View at Publisher · View at Google Scholar
13. M. Kalyna, C. G. Simpson, N. H. Syed, et al., “Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis,” Nucleic Acids Resources, vol. 40, no. 6, pp. 2454–2469, 2012. View at Publisher · View at Google Scholar
14. A. A. Hoskins and M. J. Moore, “The spliceosome: a flexible, reversible macromolecular machine,” Trends in Biochemistry Science, vol. 37, no. 5, pp. 179–188, 2012. View at Publisher · View at Google Scholar
15. Z. J. Lorković, D. A. Wieczorek Kirk, M. H. L. Lambermon, and W. Filipowicz, “Pre-mRNA splicing in higher plants,” Trends in Plant Science, vol. 5, no. 4, pp. 160–167, 2000. View at Publisher · View at Google Scholar · View at Scopus
16. M. Pertea, X. Lin, and S. L. Salzberg, “GeneSplicer: a new computational method for splice site prediction,” Nucleic Acids Research, vol. 29, no. 5, pp. 1185–1190, 2001. View at Scopus
17. S. M. Hebsgaard, P. G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouzé, and S. Brunak, “Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information,” Nucleic Acids Research, vol. 24, no. 17, pp. 3439–3452, 1996. View at Scopus
18. N. H. Syed, M. Kalyna, Y. Marquez, et al., “Alternative splicing in plants—coming of age,” Trends in Plant Science, vol. 17, no. 10, pp. 616–623, 2012.
19. W. B. Barbazuk, Y. Fu, and K. M. McGinnis, “Genome-wide analyses of alternative splicing in plants: opportunities and challenges,” Genome Research, vol. 18, no. 9, pp. 1381–1392, 2008. View at Publisher · View at Google Scholar · View at Scopus
20. L. F. Lareau, A. N. Brooks, D. A. Soergel, Q. Meng, and S. E. Brenner, “The coupling of alternative splicing and nonsense-mediated mRNA decay,” Advances in Experimental Medicine and Biology, vol. 623, pp. 190–211, 2007. View at Scopus
21. Z. Kerényi, Z. Mérai, L. Hiripi et al., “Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay,” EMBO Journal, vol. 27, no. 11, pp. 1585–1595, 2008. View at Publisher · View at Google Scholar · View at Scopus
22. X. C. Zhang and W. Gassmann, “Alternative splicing and mRNA levels of the disease resistance gene RPS4 are induced during defense responses,” Plant Physiology, vol. 145, no. 4, pp. 1577–1587, 2007. View at Publisher · View at Google Scholar · View at Scopus
23. S. Matsukura, J. Mizoi, T. Yoshida et al., “Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes,” Molecular Genetics and Genomics, vol. 283, no. 2, pp. 185–196, 2010. View at Publisher · View at Google Scholar · View at Scopus
24. D. Luo, X. Niu, Y. Wang et al., “Functional defect at the rice choline monooxygenase locus from an unusual post-transcriptional processing is associated with the sequence elements of short-direct repeats,” New Phytologist, vol. 175, no. 3, pp. 439–447, 2007. View at Publisher · View at Google Scholar · View at Scopus
25. X. Li, L. Zhao, H. Jiang, and W. Wang, “Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes,” Journal of Molecular Evolution, vol. 68, no. 1, pp. 56–65, 2009. View at Publisher · View at Google Scholar · View at Scopus
26. K. Ritz, B. D. C. van Schaik, M. E. Jakobs et al., “Looking ultra deep: short identical sequences and transcriptional slippage,” Genomics, vol. 98, no. 2, pp. 90–95, 2011. View at Publisher · View at Google Scholar · View at Scopus
27. T. Horiuchi and T. Aigaki, “Alternative trans-splicing: a novel mode of pre-mRNA processing,” Biology of the Cell, vol. 98, no. 2, pp. 135–140, 2006. View at Publisher · View at Google Scholar · View at Scopus
28. P. Akiva, A. Toporik, S. Edelheit et al., “Transcription-mediated gene fusion in the human genome,” Genome Research, vol. 16, no. 1, pp. 30–36, 2006. View at Publisher · View at Google Scholar · View at Scopus
29. R. Del Carratore, E. Magaldi, A. Podda, P. Beffy, Q. Migheli, and B. E. Maserti, “A stress responsive alternative splicing mechanism in Citrus clementina leaves,” Journal of Plant Physiology, vol. 168, no. 9, pp. 952–959, 2011. View at Publisher · View at Google Scholar · View at Scopus
30. Y. Yuan, J. D. Chung, X. Fu et al., “Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 51, pp. 22020–22025, 2009. View at Publisher · View at Google Scholar · View at Scopus
31. J. Zhang, B. Liao, D. J. Craik, J. T. Li, M. Hu, and W. S. Shu, “Identification of two suites of cyclotide precursor genes from metallophyte Viola baoshanensis: cDNA sequence variation, alternative RNA splicing and potential cyclotide diversity,” Gene, vol. 431, no. 1-2, pp. 23–32, 2009. View at Publisher · View at Google Scholar · View at Scopus
32. S. Costanzo and Y. Jia, “Alternatively spliced transcripts of Pi-ta blast resistance gene in Oryza sativa,” Plant Science, vol. 177, no. 5, pp. 468–478, 2009. View at Publisher · View at Google Scholar · View at Scopus
33. S. H. Kim, S. I. Kwon, D. Saha, N. C. Anyanwu, and W. Gassmann, “Resistance to the Pseudomonas syringae effector hopA1 is governed by the TIR-NBS-LRR Protein rps6 and is enhanced by mutations in srfr1,” Plant Physiology, vol. 150, no. 4, pp. 1723–1732, 2009. View at Publisher · View at Google Scholar · View at Scopus
34. L. Xiong and Y. Yang, “Disease resistance and abiotic stress tolerance in rice are inversely modulated by an abscisic acid-inducible mitogen-activated protein kinase,” Plant Cell, vol. 15, no. 3, pp. 745–759, 2003. View at Publisher · View at Google Scholar · View at Scopus
35. S. C. Koo, H. W. Yoon, C. Y. Kim et al., “Alternative splicing of the OsBWMK1 gene generates three transcript variants showing differential subcellular localizations,” Biochemical and Biophysical Research Communications, vol. 360, no. 1, pp. 188–193, 2007. View at Publisher · View at Google Scholar · View at Scopus
36. W. Y. Lin, D. Matsuoka, D. Sasayama, and T. Nanmori, “A splice variant of Arabidopsis mitogen-activated protein kinase and its regulatory function in the MKK6-MPK13 pathway,” Plant Science, vol. 178, no. 3, pp. 245–250, 2010. View at Publisher · View at Google Scholar · View at Scopus
37. G. P. Xue and C. W. Loveridge, “HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element,” Plant Journal, vol. 37, no. 3, pp. 326–339, 2004. View at Publisher · View at Google Scholar · View at Scopus
38. C. Egawa, F. Kobayashi, M. Ishibashi, T. Nakamura, C. Nakamura, and S. Takumi, “Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat,” Genes and Genetic Systems, vol. 81, no. 2, pp. 77–91, 2006. View at Publisher · View at Google Scholar · View at Scopus
39. F. Qin, M. Kakimoto, Y. Sakuma et al., “Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L.,” Plant Journal, vol. 50, no. 1, pp. 54–69, 2007. View at Publisher · View at Google Scholar · View at Scopus
40. A. M. Mastrangelo, S. Belloni, S. Barilli et al., “Low temperature promotes intron retention in two e-cor genes of durum wheat,” Planta, vol. 221, no. 5, pp. 705–715, 2005. View at Publisher · View at Google Scholar · View at Scopus
41. Y. Ogura, N. Ihara, A. Komatsu et al., “Gene expression, localization, and protein-protein interaction of Arabidopsis SKP1-like (ASK) 20A and 20B,” Plant Science, vol. 174, no. 5, pp. 485–495, 2008. View at Publisher · View at Google Scholar · View at Scopus
42. S. G. Palusa, G. S. Ali, and A. S. N. Reddy, “Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses,” Plant Journal, vol. 49, no. 6, pp. 1091–1107, 2007. View at Publisher · View at Google Scholar · View at Scopus
43. N. Tanabe, K. Yoshimura, A. Kimura, et al., “Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, at SR30 and at SR45a, in response to environmental stress,” Plant Cell Physiology, vol. 48, no. 7, pp. 1036–1049, 2007. View at Publisher · View at Google Scholar
44. A. S. Reddy and A. G. Shad, “Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses,” Wiley Interdisciplinary Reviews, vol. 2, no. 6, pp. 875–889, 2011. View at Publisher · View at Google Scholar
45. H. Xiao and A. Nassuth, “Stress- and development-induced expression of spliced and unspliced transcripts from two highly similar dehydrin 1 genes in V. riparia and V. vinifera,” Plant Cell Reports, vol. 25, no. 9, pp. 968–977, 2006. View at Publisher · View at Google Scholar · View at Scopus
46. A. S. Bournay, P. E. Hedley, A. Maddison, R. Waugh, and G. C. Machray, “Exon skipping induced by cold stress in a potato invertase gene transcript,” Nucleic Acids Research, vol. 24, no. 12, pp. 2347–2351, 1996. View at Publisher · View at Google Scholar · View at Scopus
47. R. Kesari, J. R. Lasky, J. G. Villamor, et al., “Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 33, pp. 9197–9202, 2012. View at Publisher · View at Google Scholar
48. H. S. Chung, T. F. Cooke, C. L. Depew et al., “Alternative splicing expands the repertoire of dominant JAZ repressors of jasmonate signaling,” Plant Journal, vol. 63, no. 4, pp. 613–622, 2010. View at Publisher · View at Google Scholar · View at Scopus
49. J. Bove, C. Y. Kim, C. A. Gibson, and S. M. Assmann, “Characterization of wound-responsive RNA-binding proteins and their splice variants in Arabidopsis,” Plant Molecular Biology, vol. 67, no. 1-2, pp. 71–88, 2008. View at Publisher · View at Google Scholar · View at Scopus
50. N. Khurana, H. Chauhan, and P. Khurana, “Expression analysis of a heat-inducible, Myo-inositol-1-phosphate synthase (MIPS) gene from wheat and the alternatively spliced variants of rice and Arabidopsis,” Plant Cell Reports, vol. 31, no. 1, pp. 237–251, 2012. View at Publisher · View at Google Scholar
51. S. Kumar, M. H. Asif, D. Chakrabarty, R. D. Tripathi, and P. K. Trivedi, “Differential expression and alternative splicing of rice sulphate transporter family members regulate sulphur status during plant growth, development and stress conditions,” Functional and Integrative Genomics, vol. 11, no. 2, pp. 259–273, 2011. View at Publisher · View at Google Scholar · View at Scopus
52. F. A. Burr, B. Burr, B. E. Scheffler, M. Blewitt, U. Wienand, and E. C. Matz, “The maize repressor-like gene intensifier1 shares homology with the r1/b1 multigene family of transcription factors and exhibits missplicing,” Plant Cell, vol. 8, no. 8, pp. 1249–1259, 1996. View at Publisher · View at Google Scholar · View at Scopus
53. R. S. McKibbin, M. D. Wilkinson, P. C. Bailey et al., “Transcripts of Vp-1 homeologues are misspliced in modern wheat and ancestral species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 15, pp. 10203–10208, 2002. View at Publisher · View at Google Scholar · View at Scopus
54. M. N. Merzlyak and O. B. Chivkunova, “Light-stress-induced pigment changes and evidence for anthocyanin photoprotection in apples,” Journal of Photochemistry and Photobiology B, vol. 55, no. 2-3, pp. 155–163, 2000. View at Publisher · View at Google Scholar · View at Scopus
55. A. Sanchez, J. Shin, and S. J. Davis, “Abiotic stress and the plant circadian clock,” Plant Signaling and Behavior, vol. 6, no. 2, pp. 223–231, 2011. View at Publisher · View at Google Scholar · View at Scopus
56. X. Niu, W. Zheng, B. R. Lu et al., “An unusual posttranscriptional processing in two betaine aldehyde dehydrogenase loci of cereal crops directed by short, direct repeats in response to stress conditions,” Plant Physiology, vol. 143, no. 4, pp. 1929–1942, 2007. View at Publisher · View at Google Scholar · View at Scopus
57. J. Fan, X. Niu, Y. Wang et al., “Short, direct repeats (SDRs)-mediated post-transcriptional processing of a transcription factor gene OsVP1 in rice (Oryza sativa),” Journal of Experimental Botany, vol. 58, no. 13, pp. 3811–3817, 2007. View at Publisher · View at Google Scholar · View at Scopus
58. E. Lazarescu, W. Friedt, and A. Steinmetz, “Organ-specific alternatively spliced transcript isoforms of the sunflower SF21C gene,” Plant Cell Reports, vol. 29, no. 7, pp. 673–683, 2010. View at Publisher · View at Google Scholar · View at Scopus
59. X. Zou, Y. Jiang, Y. Zheng, et al., “Prolyl 4-hydroxylase genes are subjected to alternative splicing in roots of maize seedlings under waterlogging,” Annals of Botany, vol. 108, no. 7, pp. 1323–1335, 2011. View at Publisher · View at Google Scholar
60. J. Li, X. Li, L. Guo et al., “A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice,” Journal of Experimental Botany, vol. 57, no. 6, pp. 1263–1273, 2006. View at Publisher · View at Google Scholar · View at Scopus
61. R. Macknight, I. Bancroft, T. Page et al., “FCA, a gene controlling flowering time in Arabidopsis, encodes a protein containing RNA-binding domains,” Cell, vol. 89, no. 5, pp. 737–745, 1997. View at Scopus
62. D. Rhodes and A. D. Hanson, “Quaternary ammonium and tertiary sulfonium compounds in higher plants,” Annual Review of Plant Physiology and Plant Molecular Biology, vol. 44, no. 1, pp. 357–384, 1993. View at Scopus
63. A. Sakamoto and N. Murata, “The role of glycine betaine in the protection of plants from stress: clues from transgenic plants,” Plant, Cell and Environment, vol. 25, no. 2, pp. 163–171, 2002. View at Publisher · View at Google Scholar · View at Scopus
64. M. Ishitani, K. Arakawa, K. Mizuno, S. Kishitani, and T. Takabe, “Betaine aldehyde dehydrogenase in the gramineae: levels in leaves both betaine-accumulating and nonaccumulating cereal plants,” Plant and Cell Physiology, vol. 34, no. 3, pp. 493–495, 1993. View at Scopus
65. N. Van Belzen, W. N. M. Dinjens, M. P. G. Diesveld et al., “A novel gene which is up-regulated during colon epithelial cell differentiation and down-regulated in colorectal neoplasms,” Laboratory Investigation, vol. 77, no. 1, pp. 85–92, 1997. View at Scopus
66. D. Piquemal, D. Joulia, P. Balaguer, A. Basset, J. Marti, and T. Commes, “Differential expression of the RTP/Drg1/Ndr1 gene product in proliferating and growth arrested cells,” Biochimica et Biophysica Acta, vol. 1450, no. 3, pp. 364–373, 1999. View at Publisher · View at Google Scholar · View at Scopus
67. F. Vlad, T. Spano, D. Vlad, F. Bou Daher, A. Ouelhadj, and P. Kalaitzis, “Arabidopsis prolyl 4-hydroxylases are differentially expressed in response to hypoxia, anoxia and mechanical wounding,” Physiologia Plantarum, vol. 130, no. 4, pp. 471–483, 2007. View at Publisher · View at Google Scholar · View at Scopus
68. M. H. Asif, P. K. Trivedi, P. Misra, and P. Nath, “Prolyl-4-hydroxylase (AtP4H1) mediates and mimics low oxygen response in Arabidopsis thaliana,” Functional and Integrative Genomics, vol. 9, no. 4, pp. 525–535, 2009. View at Publisher · View at Google Scholar · View at Scopus
69. R. Urade, “The endoplasmic reticulum stress signaling pathways in plants,” BioFactors, vol. 35, no. 4, pp. 326–331, 2009. View at Publisher · View at Google Scholar · View at Scopus
70. J. X. Liu and S. H. Howell, “Endoplasmic reticulum protein quality control and its relationship to environmental stress responses in plants,” Plant Cell, vol. 22, no. 9, pp. 2930–2942, 2010. View at Publisher · View at Google Scholar · View at Scopus
71. A. A. Moreno, M. S. Mukhtar, F. Blanco, et al., “IRE1/bZIP60-Mediated unfolded protein response plays distinct roles in plant immunity and abiotic stress responses,” PLoS ONE, vol. 7, no. 2, Article ID e31944, 2012.
72. Y. Nagashima, K. Mishiba, E. Suzuki, et al., “Arabidopsis IRE1 catalyses unconventional splicing of bZIP60 mRNA to produce the active transcription factor,” Scientific Reports, vol. 1, article 29, 2011. View at Publisher · View at Google Scholar
73. S. J. Lu, Z. T. Yang, L. Sun, et al., “Conservation of IRE1-regulated bZIP74 mRNA unconventional splicing in rice (Oryza sativa L.) involved in ER stress responses,” Molecular Plant, vol. 5, no. 2, pp. 504–514, 2012. View at Publisher · View at Google Scholar
74. S. Hayashi, Y. Wakasa, H. Takahashi, et al., “Signal transduction by IRE1-mediated splicing of bZIP50 and other stress sensors in the endoplasmic reticulum stress response of rice,” Plant Journal, vol. 69, no. 6, pp. 946–956, 2012. View at Publisher · View at Google Scholar
75. P. G. Zaphiropoulos, “Trans-splicing in higher eukaryotes: implications for cancer development?” Frontiers in Genetics, vol. 2, article 92, 2011.
76. G. Zhang, G. Guo, X. Hu et al., “Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome,” Genome Research, vol. 20, no. 5, pp. 646–654, 2010. View at Publisher · View at Google Scholar · View at Scopus
77. T. Kawasaki, S. Okumura, N. Kishimoto, H. Shimada, K. Higo, and N. Ichikawa, “RNA maturation of the rice SPK gene may involve trans-splicing,” Plant Journal, vol. 18, no. 6, pp. 625–632, 1999. View at Publisher · View at Google Scholar · View at Scopus
78. T. A. DeFalco, K. W. Bender, and W. A. Snedden, “Breaking the code: Ca²⁺ sensors in plant signalling,” Biochemical Journal, vol. 425, no. 1, pp. 27–40, 2010. View at Publisher · View at Google Scholar · View at Scopus
79. Z. S. He, H. S. Zou, Y. Z. Wang, J. B. Zhu, and G. Q. Yu, “Maturation of the nodule-specific transcript MsHSF1c in Medicago sativa may involve interallelic trans-splicing,” Genomics, vol. 92, no. 2, pp. 115–121, 2008. View at Publisher · View at Google Scholar · View at Scopus
80. A. S. Dubrovina, K. V. Kiselev, M. V. Veselova, G. A. Isaeva, S. A. Fedoreyev, and Y. N. Zhuravlev, “Enhanced resveratrol accumulation in rolB transgenic cultures of Vitis amurensis correlates with unusual changes in CDPK gene expression,” Journal of Plant Physiology, vol. 166, no. 11, pp. 1194–1206, 2009. View at Publisher · View at Google Scholar · View at Scopus
81. K. V. Kiselev, O. V. Grishchenko, and Y. N. Zhuravlev, “CDPK gene expression in salt tolerant rolB and rolC transformed cell cultures of Panax ginseng,” Biologia Plantarum, vol. 54, no. 4, pp. 621–630, 2010. View at Publisher · View at Google Scholar · View at Scopus
82. K. V. Kiselev, T. Y. Gorpenchenko, G. K. Tchernoded et al., “Calcium-dependent mechanism of somatic embryogenesis in Panax ginseng cell cultures expressing the rolC oncogene,” Molecular Biology, vol. 42, no. 2, pp. 243–252, 2008. View at Publisher · View at Google Scholar · View at Scopus
83. K. V. Kiselev, A. V. Turlenko, and Y. N. Zhuravlev, “CDPK gene expression in somatic embryos of Panax ginseng expressing rolC,” Plant Cell, Tissue and Organ Culture, vol. 99, no. 2, pp. 141–149, 2009. View at Publisher · View at Google Scholar · View at Scopus
84. D. A. Brummell, R. K. Y. Chen, J. C. Harris et al., “Induction of vacuolar invertase inhibitor mRNA in potato tubers contributes to cold-induced sweetening resistance and includes spliced hybrid mRNA variants,” Journal of Experimental Botany, vol. 62, no. 10, pp. 3519–3534, 2011. View at Publisher · View at Google Scholar · View at Scopus
85. M. B. Fasken and A. H. Corbett, “Process or perish: quality control in mRNA biogenesis,” Nature Structural and Molecular Biology, vol. 12, no. 6, pp. 482–488, 2005. View at Publisher · View at Google Scholar · View at Scopus
86. O. Mühlemann, A. B. Eberle, L. Stalder, and R. Zamudio Orozco, “Recognition and elimination of nonsense mRNA,” Biochimica et Biophysica Acta, vol. 1779, no. 9, pp. 538–549, 2008. View at Publisher · View at Google Scholar · View at Scopus
87. S. Kertész, Z. Kerényi, Z. Mérai et al., “Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants,” Nucleic Acids Research, vol. 34, no. 21, pp. 6147–6157, 2006. View at Publisher · View at Google Scholar · View at Scopus
88. B. P. Lewis, R. E. Green, and S. E. Brenner, “Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 1, pp. 189–192, 2003. View at Publisher · View at Google Scholar · View at Scopus
89. K. D. Hansen, L. F. Lareau, M. Blanchette et al., “Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila,” PLoS Genetics, vol. 5, no. 6, Article ID e1000525, 2009. View at Publisher · View at Google Scholar · View at Scopus
90. A. K. Ramani, A. C. Nelson, P. Kapranov, I. Bell, T. R. Gingeras, and A. G. Fraser, “High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans,” Genome Biology, vol. 10, no. 9, article R101, 2009. View at Publisher · View at Google Scholar · View at Scopus
91. S. G. Palusa and A. S. N. Reddy, “Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay,” New Phytologist, vol. 185, no. 1, pp. 83–89, 2010. View at Publisher · View at Google Scholar · View at Scopus
92. A. Sugio, R. Dreos, F. Aparicio, and A. J. Maule, “The cytosolic protein response as a subcomponent of the wider heat shock response in Arabidopsis,” Plant Cell, vol. 21, no. 2, pp. 642–654, 2009. View at Publisher · View at Google Scholar · View at Scopus
93. H. J. Jeong, Y. J. Kim, S. H. Kim, et al., “Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense,” Plant Cell Physiology, vol. 52, no. 12, pp. 2147–2156, 2011. View at Publisher · View at Google Scholar
94. S. Rayson, L. Arciga-Reyes, L. Wootton, et al., “A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants,” PLoS ONE, vol. 7, no. 2, Article ID e31917, 2012.
95. E. Gilboa, S. W. Mitra, S. Goff, and D. Baltimore, “A detailed model of reverse transcription and tests of crucial aspects,” Cell, vol. 18, no. 1, pp. 93–100, 1979. View at Scopus
96. G. Luo and J. Taylor, “Template switching by reverse transcriptase during DNA synthesis,” Journal of Virology, vol. 64, no. 9, pp. 4321–4328, 1990. View at Scopus
97. J. Cocquet, A. Chong, G. Zhang, and R. A. Veitia, “Reverse transcriptase template switching and false alternative transcripts,” Genomics, vol. 88, no. 1, pp. 127–131, 2006. View at Publisher · View at Google Scholar · View at Scopus
98. S. W. Roy and M. Irimia, “When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis,” BioEssays, vol. 30, no. 6, pp. 601–605, 2008. View at Publisher · View at Google Scholar · View at Scopus
99. J. Houseley and D. Tollervey, “Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro,” PLoS ONE, vol. 5, no. 8, Article ID e12271, 2010. View at Publisher · View at Google Scholar · View at Scopus
100. M. Ouhammouch and E. N. Brody, “Temperature-dependent template switching during in vitro cDNA synthesis by the AMV-reverse transcriptase,” Nucleic Acids Research, vol. 20, no. 20, pp. 5443–5450, 1992. View at Scopus
101. R. M. Mader, W. M. Schmidt, R. Sedivy et al., “Reverse transcriptase template switching during reverse transcriptase-polymerase chain reaction: artificial generation of deletions in ribonucleotide reductase mRNA,” Journal of Laboratory and Clinical Medicine, vol. 137, no. 6, pp. 422–428, 2001. View at Publisher · View at Google Scholar · View at Scopus
102. X. C. Zeng and S. X. Wang, “Evidence that BmTXKβ-BmKCT cDNA from Chinese scorpion Buthus martensii Karsch is an artifact generated in the reverse transcription process,” FEBS Letters, vol. 520, no. 1–3, pp. 183–184, 2002. View at Publisher · View at Google Scholar · View at Scopus
103. M. Geiszt, K. Lekstrom, and T. L. Leto, “Analysis of mRNA transcripts from the NAD(P)H oxidase 1 (Nox1) gene: evidence against production of the NADPH oxidase homolog-1 short (NOH-1s) transcript variant,” Journal of Biological Chemistry, vol. 279, no. 49, pp. 51661–51668, 2004. View at Publisher · View at Google Scholar · View at Scopus
104. K. A. Delviks and V. K. Pathak, “Effect of distance between homologous sequences and 3' homology on the frequency of retroviral reverse transcriptase template switching,” Journal of Virology, vol. 73, no. 10, pp. 7923–7932, 1999. View at Scopus
105. J. A. Shapiro, Evolution: A View from the 21st Century, FT Press Science, Upper Saddle River, NJ, USA, 2011.
106. M. Drenthen, J. Keulartz, and J. Proctor, Eds., New Visions of Nature: Complexity and Authenticity, Springer, London, UK, 2009.
107. G. P. Dubey and S. Ben-Yehuda, “Intercellular nanotubes mediate bacterial communication,” Cell, vol. 144, no. 4, pp. 590–600, 2011. View at Publisher · View at Google Scholar · View at Scopus
108. H. C. Fan, W. Gu, J. Wang, et al., “Non-invasive prenatal measurement of the fetal genome,” Nature, vol. 487, no. 7407, pp. 320–324, 2012. View at Publisher · View at Google Scholar
109. S. Stegemann and R. Bock, “Exchange of genetic material between cells in plant tissue grafts,” Science, vol. 324, no. 5927, pp. 649–651, 2009. View at Publisher · View at Google Scholar · View at Scopus
110. A. Molnar, C. W. Melnyk, A. Bassett, T. J. Hardcastle, R. Dunn, and D. C. Baulcombe, “Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells,” Science, vol. 328, no. 5980, pp. 872–875, 2010. View at Publisher · View at Google Scholar · View at Scopus