25 Quevillon E, Silventoinen V, Pillai S, et al. InterProScan: protein domains identifier. Nucleic Acids Res, 2005, 33: W116-W120
[2]
26 Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012, 7: 562-578
[3]
27 Rabbitts T H. Evidence for splicing of interrupted immunoglobulin variable and constant region sequences in nuclear RNA. Nature, 1978, 275: 291-296
[4]
28 Black D L. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem, 2003, 72: 291-336
[5]
29 Stamm S, Ben-Ari S, Rafalska I, et al. Function of alternative splicing. Gene, 2005, 344: 1-20
[6]
30 Lareau L F, Green R E, Bhatnagar R S, et al. The evolving roles of alternative splicing. Curr Opin Struc Biol, 2004, 14: 273-282
[7]
31 Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res, 2002, 30: 3754-3766
[8]
32 Transcriptome and genome conservation of alternative splicing events in humans and mice. In: Sugnet C W, Kent W J, Haussler D, eds. Proc. 9th Pacific Symposium on Biocomputing. Hawaii. 2004, Singapore: World Scientific, 2004. 66-77
[9]
33 Chacko E, Ranganathan S. Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases. BMC Genomics, 2009, 10: S11
[10]
34 Babenko V N, Aitnazarov R B, Goncharov F A, et al. Alternative splicing landscape of the Drosophila melanogaster genome. Russ J Genet, 2010, 46: 1036-1038
[11]
35 Labadorf A, Link A, Rogers M F, et al. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics, 2010, 11: 114
[12]
36 Ramani A K, Calarco J A, Pan Q, et al. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res, 2011, 21: 342-348
[13]
37 Sablok G, Gupta P K, Baek J M, et al. Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics. Biotechnol Lett, 2011, 33: 629-636
[14]
38 Bao H, Li E Y, Mansfield S D, et al. The developing xylem transcriptome and genome-wide analysis of alternative splicing in Populus trichocarpa (black cottonwood) populations. BMC Genomics, 2013, 14: 359
[15]
39 Panahi B, Abbaszadeh B, Taghizadeghan M, et al. Genome-wide survey of alternative splicing in Sorghum Bicolor. Physiol Mol Biol Plants, 2014, 20: 323-329
[16]
40 Wu H P, Su Y S, Chen H C, et al. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol, 2014, 15: R10
[17]
41 Shen Y, Zhou Z, Wang Z, et al. Global dissection of alternative splicing in paleopolyploid soybean. Plant Cell, 2014, 26: 996-1008
[18]
42 Li P, Ponnala L, Gandotra N, et al. The developmental dynamics of the maize leaf transcriptome. Nat Genet, 2010, 42: 1060-1067
[19]
43 Marquez Y, Brown J W, Simpson C, et al. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res, 2012, 22: 1184-1195
[20]
44 Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet, 2008, 40: 1413-1415
[21]
45 Walters B, Lum G, Sablok G, et al. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res, 2013, 20: 163-171
[22]
46 Baek J M, Han P, Iandolino A, et al. Characterization and comparison of intron structure and alternative splicing between Medicago truncatula, Populus trichocarpa, Arabidopsis and rice. Plant Mol Biol, 2008, 67: 499-510
[23]
47 Staiger C J. Signaling to the actin cytoskeleton in plants. Annu Rev Plant Physiol Plant Mol Biol, 2000, 51: 257-288
[24]
48 Kadota A, Wada M. Photoorientation of chloroplasts in protonemal cells of the fernAdiantum as analyzed by use of a video-tracking system. Bot Mag, 1992, 105: 265-279
[25]
49 Wada M, Kagawa T, Sato Y. Chloroplast movement. Annu Rev Plant Biol, 2003, 54: 455-468
[26]
50 Stock A M, Robinson V L, Goudreau P N. Two-component signal transduction. Annu Rev Biochem, 2000, 69: 183-215
1 Arcus A C. Proteolytic enzyme of Actinidia chinensis. Biochim Biophys Acta, 1959, 33: 242-244
[34]
2 Cheng C H, Seal A G, Boldingh H L, et al. Inheritance of taste characters and fruit size and number in a diploid Actinidia chinensis (kiwifruit) population. Euphytica, 2004, 138: 185-195
[35]
3 Skinner M A, Loh J M S, Hunter D C, et al. Gold kiwifruit (Actinidia chinensis ‘Hort16A'') for immune support. Proc Nutr Soc, 2011, 70: 276-280
6 Wang B B, Brendel V. Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci USA, 2006, 103: 7175-7180
[39]
7 Huang S, Ding J, Deng D, et al. Draft genome of the kiwifruit Actinidia chinensis. Nat Commun, 2013, 4: 2640
[40]
8 Berget S M, Moore C, Sharp P A. Spliced segments at the 5'' terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA, 1977, 74: 3171-3175
[41]
9 Tong C, Wang X, Yu J, et al. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics, 2013, 14: 689
[42]
10 Reddy A S. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol, 2007, 58: 267-294
[43]
11 Zhang G, Guo G, Hu X, et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res, 2010, 20: 646-654
[44]
12 Reddy A S, Marquez Y, Kalyna M, et al. Complexity of the alternative splicing landscape in plants. Plant Cell, 2013, 25: 3657-3683
[45]
13 Zhang X N, Mount S M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiol, 2009, 150: 1450-1458
[46]
14 Wang Q, Silver P A. Genome-wide RNAi screen discovers functional coupling of alternative splicing and cell cycle control to apoptosis regulation. Cell Cycle, 2010, 9: 4419-4421
[47]
15 Gu L, Guo R. Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice. J genet genomics, 2007, 34: 247-257
[48]
16 Leviatan N, Alkan N, Leshkowitz D, et al. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PLoS One, 2013, 8: e66511
[49]
17 Staiger D, Brown J W. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell, 2013, 25: 3640-3656
[50]
18 Quesada V, Macknight R, Dean C, et al. Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J, 2003, 22: 3142-3152
[51]
19 Ding F, Cui P, Wang Z Y, et al. Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis. BMC Genomics, 2014, 15: 431
[52]
20 Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature, 2008, 456: 470-476
[53]
21 Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res, 2010, 20: 45-58
[54]
22 Goldberg D H, Victor J D, Gardner E P, et al. Spike train analysis toolkit: enabling wider application of information-theoretic techniques to neurophysiology. Neuroinformatics, 2009, 7: 165-178
[55]
23 Patel R K, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One, 2012, 7: e30619
[56]
24 Trapnell C, Pachter L, Salzberg S L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, 25: 1105-1111