title: mRNA-seq analysis of the Gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage.
abstract: The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H(2)O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts' response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences, Anyang, Henan, China.
authors: Xueyan
authors: X
authors: Zhang
authors: Dongxia
authors: D
authors: Yao
authors: Qianhua
authors: Q
authors: Wang
authors: Wenying
authors: W
authors: Xu
authors: Qiang
authors: Q
authors: Wei
authors: Chunchao
authors: C
authors: Wang
authors: Chuanliang
authors: C
authors: Liu
authors: Chaojun
authors: C
authors: Zhang
authors: Hong
authors: H
authors: Yan
authors: Yi
authors: Y
authors: Ling
authors: Zhen
authors: Z
authors: Su
authors: Fuguang
authors: F
authors: Li
mesh_terms: D016000:Cluster Analysis; D003681:Dehydration; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D023061:Gene Order; D003368:Gossypium / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D010937:Plant Growth Regulators / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018547:Plant Stems / Q000235:genetics / Q000378:metabolism; D011092:Polyethylene Glycols / Q000494:pharmacology; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D036226:Seedlings / Q000235:genetics*; D015398:Signal Transduction / Q000187:drug effects; D012965:Sodium Chloride / Q000494:pharmacology; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010937:Plant Growth Regulators; D014157:Transcription Factors; D011092:Polyethylene Glycols; D012965:Sodium Chloride
references: Science. 2009 May 22;324(5930):1068-71
references: 19407142
references: BMC Plant Biol. 2010 Aug 05;10:160
references: 20687943
references: Curr Opin Plant Biol. 2011 Jun;14(3):290-5
references: 21377404
references: BMC Res Notes. 2009 Jul 02;2:120
references: 19570239
references: Plant Physiol. 2010 Apr;152(4):1787-95
references: 20118272
references: Plant Physiol. 1981 Mar;67(3):489-93
references: 16661700
references: Cell Res. 2005 Oct;15(10):796-810
references: 16246269
references: Plant Sci. 2011 Mar;180(3):461-9
references: 21421393
references: Nature. 2009 Dec 3;462(7273):665-8
references: 19898494
references: Plant Physiol. 1984 Oct;76(2):392-4
references: 16663851
references: Plant Cell. 2010 Jun;22(6):2058-84
references: 20587772
references: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W64-70
references: 20435677
references: Curr Opin Plant Biol. 2003 Oct;6(5):441-5
references: 12972044
references: Plant Physiol. 2011 May;156(1):430-8
references: 21402795
references: Funct Integr Genomics. 2008 Aug;8(3):277-86
references: 18320247
references: Plant Mol Biol. 2005 Jul;58(5):699-720
references: 16158244
references: J Exp Bot. 2006;57(5):1097-107
references: 16510518
references: Plant Cell Environ. 2010 Apr;33(4):648-54
references: 20002333
references: Plant Physiol. 1982 Mar;69(3):609-13
references: 16662258
references: Annu Rev Plant Biol. 2010;61:651-79
references: 20192755
references: Science. 2008 Aug 15;321(5891):956-60
references: 18599741
references: Nature. 2009 Dec 3;462(7273):660-4
references: 19924127
references: BMC Plant Biol. 2006 Oct 12;6:25
references: 17038189
references: Science. 2008 May 16;320(5878):942-5
references: 18436742
references: Plant Cell. 2001 Apr;13(4):889-905
references: 11283343
references: Cell. 2008 May 2;133(3):523-36
references: 18423832
references: Plant J. 2011 Feb;65(4):503-16
references: 21208307
references: J Plant Physiol. 2008 Mar 13;165(4):375-84
references: 17686549
references: Plant Physiol. 1965 Mar;40(2):229-34
references: 16656078
references: Genome Res. 2010 May;20(5):646-54
references: 20305017
references: Plant Mol Biol. 2010 Jan;72(1-2):27-45
references: 19806323
references: Nature. 2008 Jun 26;453(7199):1239-43
references: 18488015
references: Genome Biol. 2010;11(12):220
references: 21176179
references: Plant Physiol. 2010 Jan;152(1):133-50
references: 19889877
references: Mol Biol Rep. 2012 Feb;39(2):1011-8
references: 21556756
references: Plant Physiol. 1986 Nov;82(3):724-8
references: 16665100
references: Annu Rev Plant Physiol Plant Mol Biol. 2000 Jun;51:463-499
references: 15012199
references: Plant Mol Biol. 2002 Mar-Apr;48(5-6):551-73
references: 11999834
references: Plant Physiol. 2002 Dec;130(4):2129-41
references: 12481097
references: Plant Mol Biol. 2009 Mar;69(4):451-62
references: 19031047
references: Methods Enzymol. 2007;428:419-38
references: 17875432
references: Plant Physiol. 2009 Dec;151(4):1902-17
references: 19812185
references: Plant Physiol. 2004 Jul;135(3):1697-709
references: 15247402
references: Nat Protoc. 2010 Feb;5(2):255-66
references: 20134426
references: Plant Physiol. 1991 Feb;95(2):628-35
references: 16668029
references: Genome Res. 2010 Sep;20(9):1238-49
references: 20627892
references: Annu Rev Plant Biol. 2008;59:651-81
references: 18444910
references: Plant Physiol. 1982 Jul;70(1):238-43
references: 16662453
references: Biotechnol Prog. 2010 Jan-Feb;26(1):21-5
references: 19847887
references: Plant Physiol. 1987 Aug;84(4):1154-7
references: 16665577
references: Genome Res. 2007 Nov;17(11):1614-25
references: 17921353
references: Curr Opin Plant Biol. 2011 Jun;14(3):296-302
references: 21511515
references: Science. 2008 Jun 6;320(5881):1344-9
references: 18451266
references: Plant Physiol. 2007 Feb;143(2):707-19
references: 17189334
references: Genome Res. 2010 Feb;20(2):265-72
references: 20019144
references: Annu Rev Plant Biol. 2002;53:247-73
references: 12221975
references: Genome Res. 1997 Oct;7(10):986-95
references: 9331369
references: Plant Physiol. 1975 Nov;56(5):595-9
references: 16659351
references: Bioinformatics. 2005 Sep 15;21(18):3674-6
references: 16081474
references: Tanpakushitsu Kakusan Koso. 1999 Nov;44(15 Suppl):2186-7
references: 10586655
references: Plant Cell Environ. 2010 Apr;33(4):543-51
references: 19843253
references: Plant J. 2010 Jan;61(2):290-9
references: 19874541
references: Nat Methods. 2008 Jul;5(7):621-8
references: 18516045
references: Theor Appl Genet. 2006 May;112(7):1286-94
references: 16496119
references: Science. 2009 May 22;324(5930):1064-8
references: 19407143
references: Genomics. 2011 Jul;98(1):47-55
references: 21569837
references: Biotechnol Lett. 2010 Oct;32(10):1361-71
references: 20502944
references: Nature. 2011 Mar 24;471(7339):473-9
references: 21179090
references: Curr Opin Cell Biol. 2001 Aug;13(4):399-404
references: 11454443
references: EMBO Rep. 2009 Aug;10(8):923-8
references: 19575013
references: Genome Res. 2010 Jan;20(1):45-58
references: 19858364
references: Nat Genet. 2012 Oct;44(10):1098-103
references: 22922876
references: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references: 10786296
references: Proc Natl Acad Sci U S A. 1974 Aug;71(8):3243-7
references: 4528731