title: RNA sequencing analysis reveals transcriptomic variations in tobacco (Nicotiana tabacum) leaves affected by climate, soil, and tillage factors.
abstract: The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. leibo198109@gmail.com.
authors.forename: Bo
authors.initials: B
authors.lastname: Lei
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. drlukun@swu.edu.cn.
authors.forename: Kun
authors.initials: K
authors.lastname: Lu
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. dingfuzhang2014@gmail.com.
authors.forename: Fuzhang
authors.initials: F
authors.lastname: Ding
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. kaizhang2013@gmail.com.
authors.forename: Kai
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. chenyi83829@gmail.com.
authors.forename: Yi
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. zhaohn1983@gmail.com.
authors.forename: Huina
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. zhanglin02150215@gmail.com.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. bambooren1211@gmail.com.
authors.forename: Zhu
authors.initials: Z
authors.lastname: Ren
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. drqucunmin@swu.edu.cn.
authors.forename: Cunmin
authors.initials: C
authors.lastname: Qu
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. guowenjing0725@gmail.com.
authors.forename: Wenjing
authors.initials: W
authors.lastname: Guo
authors.affiliation: Engineering Research Center of South Upland Agriculture, College of Agronomy and Biotechnology, Southwest University, Tiansheng Road 2, Beibei, Chongqing 400715, China. wangjing217324@gmail.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Molecular Genetics, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Longbatan Road 29, Guanshanhu District, Guiyang 550081, China. panwenjie@gmail.com.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Pan
mesh_terms: D002940:Circadian Rhythm / Q000502:physiology; D002980:Climate; D020869:Gene Expression Profiling; D010788:Photosynthesis; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D025341:Principal Component Analysis; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012987:Soil / Q000737:chemistry*; D014026:Nicotiana / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome
chemical_list: D012987:Soil; D012313:RNA
references.citation: Plant Cell. 2010 Mar;22(3):594-605
references.pmid: 20233950
references.citation: Plant Physiol. 2012 Oct;160(2):846-67
references.pmid: 22837360
references.citation: Science. 1998 May 15;280(5366):1091-4
references.pmid: 9582125
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W316-22
references.pmid: 21715386
references.citation: Cell. 2012 Dec 7;151(6):1358-69
references.pmid: 23217716
references.citation: Bioinformatics. 2004 Nov 22;20(17):3246-8
references.pmid: 15180930
references.citation: Cell. 2012 Dec 7;151(6):1161-2
references.pmid: 23217702
references.citation: Plant Sci. 2000 Oct 16;159(1):159-167
references.pmid: 11011103
references.citation: Trends Plant Sci. 2012 Mar;17(3):172-9
references.pmid: 22236698
references.citation: Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7241-6
references.pmid: 21471455
references.citation: Plant J. 2010 Feb;61(4):672-85
references.pmid: 19947981
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1149-55
references.pmid: 20935049
references.citation: Genome Biol. 2013 Jun 07;14(6):r54
references.pmid: 23759170
references.citation: Bioinformatics. 2012 Jan 15;28(2):282-3
references.pmid: 22113082
references.citation: Plant Physiol. 2002 Nov;130(3):1143-51
references.pmid: 12427981
references.citation: Bioinformatics. 2011 Feb 1;27(3):431-2
references.pmid: 21149340
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Bioinformatics. 2004 Jun 12;20(9):1453-4
references.pmid: 14871861
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11698-703
references.pmid: 21709243
references.citation: Mol Biol Rep. 2013 Jan;40(1):345-57
references.pmid: 23079704
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Plant Physiol. 2004 Apr;134(4):1683-96
references.pmid: 15047901
references.citation: Plant Physiol. 2013 Feb;161(2):705-24
references.pmid: 23197803
references.citation: Dev Cell. 2002 May;2(5):629-41
references.pmid: 12015970
references.citation: Nat Protoc. 2012 Mar 01;7(3):562-78
references.pmid: 22383036
references.citation: BMC Biol. 2011 May 31;9:34
references.pmid: 21627854
references.citation: BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S5
references.pmid: 22165852
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: DNA Seq. 1998;9(5-6):329-33
references.pmid: 10524760
references.citation: Bioinformatics. 2005 Aug 15;21(16):3448-9
references.pmid: 15972284
references.citation: BMC Genomics. 2011 Oct 18;12:514
references.pmid: 22008187
references.citation: Plant Sci. 2011 Apr;180(4):562-74
references.pmid: 21421405
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Methods. 2001 Dec;25(4):402-8
references.pmid: 11846609
references.citation: BMC Genomics. 2010 Feb 26;11:142
references.pmid: 20187945
references.citation: J Integr Plant Biol. 2009 Jul;51(7):663-74
references.pmid: 19566645
references.citation: Mol Genet Genomics. 2010 Mar;283(3):233-41
references.pmid: 20098998
references.citation: Theor Appl Genet. 2008 Oct;117(6):963-75
references.pmid: 18716755
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1202-10
references.pmid: 22140109