title: Evolutionary Character of Alternative Splicing in Plants.
abstract: Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. What is the content rate of AS genes among the whole gene set? How many AS types are presented in the genome, and which type is dominant? How about the conservation ability of AS among different species? Which kinds of isoforms from some genes have the environmental response to help individual adaptation? Based on this background, we collected analysis results from 17 species to try to map out the landscape of AS studies in plants. We have noted the shortages of previous results, and we appeal to all scientists working in the AS field to make a standard protocol so that analyses between different projects are comparable.
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.
authors.forename: Chengjun
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yang
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China.
authors.forename: Huizhao
authors.initials: H
authors.lastname: Yang
keywords: alternative splicing; comparative analyses; conservation ability; stress response
references.citation: Bioinformatics. 2015 Oct 15;31(20):3359-61
references.pmid: 26069263
references.citation: BMC Genomics. 2010 Mar 30;11:210
references.pmid: 20350329
references.citation: Proc Natl Acad Sci U S A. 1977 Aug;74(8):3171-5
references.pmid: 269380
references.citation: Mol Plant. 2014 May;7(5):829-40
references.pmid: 24398628
references.citation: Nature. 2011 Mar 24;471(7339):473-9
references.pmid: 21179090
references.citation: Plant Cell. 2015 Jan;27(1):71-85
references.pmid: 25634987
references.citation: Plant Physiol. 2003 Jun;132(2):469-84
references.pmid: 12805580
references.citation: Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):16122-7
references.pmid: 21900601
references.citation: BMC Genomics. 2013 May 29;14:359
references.pmid: 23718132
references.citation: Physiol Mol Biol Plants. 2014 Jul;20(3):323-9
references.pmid: 25049459
references.citation: Nucleic Acids Res. 2007;35(1):125-31
references.pmid: 17158149
references.citation: Genome Res. 2010 Jan;20(1):45-58
references.pmid: 19858364
references.citation: Dev Cell. 2015 Apr 6;33(1):107-18
references.pmid: 25850675
references.citation: RNA. 2004 May;10(5):757-65
references.pmid: 15100430
references.citation: Nat Rev Mol Cell Biol. 2005 May;6(5):386-98
references.pmid: 15956978
references.citation: BMC Genomics. 2006 Dec 28;7:327
references.pmid: 17194304
references.citation: BMC Bioinformatics. 2014 Dec 16;15:364
references.pmid: 25511303
references.citation: Plant Physiol. 2014 Apr 28;165(2):826-840
references.pmid: 24777346
references.citation: DNA Res. 2013 Apr;20(2):163-71
references.pmid: 23297300
references.citation: Plant Physiol. 2007 Jul;144(3):1632-41
references.pmid: 17496110
references.citation: PLoS One. 2013 Jun 11;8(6):e66511
references.pmid: 23776682
references.citation: BMC Plant Biol. 2014 May 19;14:136
references.pmid: 24885185
references.citation: Genome Res. 2012 Jun;22(6):1184-95
references.pmid: 22391557
references.citation: Genome Res. 2002 Dec;12(12):1837-45
references.pmid: 12466287
references.citation: Genome Res. 2010 Sep;20(9):1238-49
references.pmid: 20627892
references.citation: Science. 2004 Oct 22;306(5696):655-60
references.pmid: 15499012
references.citation: New Phytol. 2013 Jul;199(1):252-63
references.pmid: 23551259
references.citation: Genome Res. 2010 May;20(5):646-54
references.pmid: 20305017
references.citation: Plant Cell. 2014 Sep;26(9):3472-87
references.pmid: 25248552
references.citation: BMC Plant Biol. 2008 Feb 19;8:17
references.pmid: 18282305
references.citation: Genome Biol. 2014 Jan 07;15(1):R10
references.pmid: 24398233
references.citation: BMC Genomics. 2009 Apr 09;10:154
references.pmid: 19358722
references.citation: BMC Genomics. 2014 Jun 04;15:431
references.pmid: 24897929
references.citation: BMC Genomics. 2014 Sep 10;15:780
references.pmid: 25209012
references.citation: Nat Rev Genet. 2004 Oct;5(10):773-82
references.pmid: 15510168
references.citation: PLoS One. 2013 Oct 01;8(10):e74183
references.pmid: 24098335
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: Cell. 1977 Sep;12(1):1-8
references.pmid: 902310
references.citation: Bioessays. 2012 Nov;34(11):982-91
references.pmid: 23001763
references.citation: Science. 2008 Sep 5;321(5894):1357-61
references.pmid: 18772439
references.citation: Plant J. 2004 Sep;39(6):877-85
references.pmid: 15341630
references.citation: Nat Rev Genet. 2010 May;11(5):345-55
references.pmid: 20376054
references.citation: Nat Rev Genet. 2013 Sep;14(9):645-60
references.pmid: 23949544
references.citation: Proc Natl Acad Sci U S A. 2006 May 2;103(18):7175-80
references.pmid: 16632598
references.citation: Proc Natl Acad Sci U S A. 1980 Apr;77(4):1877-9
references.pmid: 6246511
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):22020-5
references.pmid: 19996170
references.citation: Nature. 1980 Aug 21;286(5775):776-9
references.pmid: 6772972
references.citation: Nucleic Acids Res. 2004 Sep 27;32(17):5096-103
references.pmid: 15452276
references.citation: Plant Physiol. 2014 May;165(1):412-23
references.pmid: 24520158
references.citation: Plant Cell. 2015 Mar;27(3):513-31
references.pmid: 25783031
references.citation: BMC Plant Biol. 2014 Apr 17;14:99
references.pmid: 24739459
references.citation: Plant Cell. 1989 Aug;1(8):815-25
references.pmid: 2535524
references.citation: Nat Genet. 2008 Dec;40(12):1413-5
references.pmid: 18978789
references.citation: Nucleic Acids Res. 2010 Aug;38(14):4740-54
references.pmid: 20385588
references.citation: Gene. 2005 Dec 30;364:53-62
references.pmid: 16219431
references.citation: Proc Biol Sci. 1994 May 23;256(1346):119-24
references.pmid: 8029240
references.citation: PLoS Genet. 2014 Dec 04;10(12):e1004843
references.pmid: 25474210
references.citation: Plant Cell. 2012 Mar;24(3):961-81
references.pmid: 22408072
references.citation: Plant Cell. 2014 Mar;26(3):996-1008
references.pmid: 24681622