Response of Chinese fir seedlings to low phosphorus stress and analysis of gene expression differences
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摘要
Chinese fir(Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus(LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity,proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups(CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software,607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.
Chinese fir(Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus(LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity,proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups(CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software,607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.
Chinese fir(Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus(LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity,proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups(CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software,607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.
引文
Audic S,Claverie J-M(1997)The significance of digital gene expression profiles.Genome Res 7:986-995
Benjamini Y,Yekutieli D(2001)The control of the false discovery rate in multiple testing under dependency.Ann Stat29:1165-1188
Bian L,Zheng R,Su S,Lin H,Xiao H,Wu HX,Shi J(2017)Spatial analysis increases efficiency of progeny testing of chinese fir.J For Res 28(3):445-452
Bozzo GG,Raghothama KG,Plaxton WC(2003)Purification and characterization of two secreted purple acid phosphatase isozymes from phosphate-starved tomato(Lycopersicon esculentum)cell cultures.Eur J Biochem 269:6278-6286
Chen FJ,Liu XS,Guo-Hua MI(2012)Varietal differences in plant growth,phosphorus uptake and yield formation in two maize inbred lines grown under field conditions.J Integr Agric11:1738-1743
Coelho GTCP,Carneiro NP,Karthikeyan AS,Raghothama KG,Schaffert RE,Brandao RL,Paiva LV,Souza IRP,Alves VM,Imolesi A(2010)A phosphate transporter promoter from Arabidopsis thaliana AtPHT1;4 gene drives preferential gene expression in transgenic maize roots under phosphorus starvation.Plant Mol Biol Report 28:717-723
Conesa A,Gotz S,Garc?a-Gomez JM,Terol J,Talon M,Robles M(2005)Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research.Bioinformatics21:3674-3676
Duan H,Hu D,Li Y,Zheng H(2016)Characterization of a collection of chinese fir elite genotypes using sequence-related amplified polymorphism markers.J For Res 27(5):1-6
Dubey NC,Tripathi BP,Muller M,Stamm M,Ionov L(2015)Enhanced activity of acetyl CoA synthetase adsorbed on smart microgel:an implication for precursor biosynthesis.ACS Appl Mater Interface 7:1500-1507
Fan F,Ding G,Wen X(2016)Proteomic analyses provide new insights into the responses of Pinus massoniana seedlings to phosphorus deficiency.Proteomics 16(3):504-515
Fort F,Cruz P,Stroia C,Jouany C,Catrice O,Delbrut A,Luzarreta M(2015)Root functional trait syndromes and plasticity drive the ability of grassland Fabaceae to tolerate water and phosphorus shortage.Environ Exp Bot 110:62-72
Gilbert GA,Knight JD,Vance CP,Allan DL(1999)Acid phosphatase activity in phosphorus-deficient white lupin roots.Plant Cell Environ 22(7):801-810
Guo B,Irigoyen S,Fowler TB,Versaw WK(2008)Differential expression and phylogenetic analysis suggest specialization of plastid-localized members of the PHT4 phosphate transporter family for photosynthetic and heterotrophic tissues.Plant Signal Behav 3:784-790
Hammond JP,Broadley MR,Bowen HC,Spracklen WP,Hayden RM,White PJ(2011)Gene expression changes in phosphorus deficient potato(Solanum teubrosum L.)leaves and the potential for diagnostic gene expression markers.PLoS ONE 6(9):e24606
He P,Qin H,Wu M,Wu B,Wei J,Wang D(2013)Identification of genes differentially expressed in the roots of rubber tree(Hevea brasiliensis Muell.Arg.)in response to phosphorus deficiency.Mol Biol Rep 40:1397-1405
Lapis-Gaza HR,Jost R,Finnegan PM(2014)Arabidopsis PHOS-PHATE TRANSPORTER1 genes PHT1;8 and PHT1;9 are involved in root-to-shoot translocation of orthophosphate.BMCPlant Biol 14:1-19
Li L,Liu C,Lian X(2010)Gene expression profiles in rice roots under low phosphorus stress.Plant Mol Biol 72:423-432
Li S,Ha SJ,Kim HJ,Galazka JM,Cate JHD,Jin YS,Zhao H(2013)Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization.J Biotechnol 168:1-6
Lu Yong-quan,Jia Qing,Tong Zai-kang(2014)Cloning and sequence analysis of nine novel MYB genes in Taxodiaceae plants.J For Res 25(4):795-804
Ma Z,Huang B,Xu S,Chen Y,Cao G,Ding G,Lin S(2016)Ion flux in roots of Chinese fir(Cunninghamia lanceolata(Lamb.)Hook)under aluminum stress.PLoS ONE 11:e0156832
Marschner H(1995)Mineral nutrition of higher plants,2nd edn.Academic Press,London
Miguel MA,Widrig A,Vieira RF,Brown KM,Lynch JP(2013)Basal root whorl number:a modulator of phosphorus acquisition in common bean(Phaseolus vulgaris).Ann Bot 112:973-982
Mortazavi A,Williams BA,McCue K,Schaeffer L,Wold B(2008)Mapping and quantifying mammalian transcriptomes by RNA-Seq.Nat Methods 5:621-628
Orwa C,Mutua A,Kindt R,Jamnadass R,Simons A(2015)Agroforestree database:a tree reference and selection guide version 4.0.2009.http://www.worldagroforestry.org/af/treedb/.Accessed 15 Feb 2011
Rausch C,Zimmermann P,Amrhein N,Bucher M(2004)Expression analysis suggests novel roles for the plastidic phosphate transporter Pht2;1 in auto-and heterotrophic tissues in potato and Arabidopsis.Plant J 39:13-28
Richardson AE,Lynch JP,Ryan PR,Delhaize E,Smith FA,Smith SE,Harvey PR,Ryan MH,Veneklaas EJ,Lambers H(2011)Plant and microbial strategies to improve the phosphorus efficiency of agriculture.Plant Soil 349:121-156
Rouached H,Arpat AB,Poirier Y(2010)Regulation of phosphate starvation responses in plants:signaling players and cross-talks.Mol Plant 3:288-299
Saldanha AJ(2004)Java Treeview-extensible visualization of microarray data.Bioinformatics 20:3246-3248
Sharma V,Kumar A,Archana G,Kumar GN(2016)Ensifermeliloti overexpressing Escherichia coli phytase gene(appA)improves phosphorus(P)acquisition in maize plants.Sci Nat 103:76
Simpson RJ,Oberson A,Culvenor RA,Ryan MH,Veneklaas EJ,Lambers H,Lynch JP,Ryan PR,Delhaize E,Smith FA(2011)Strategies and agronomic interventions to improve the phosphorus-use efficiency of farming systems.Plant Soil 349:89-120
Vance CP,Uhde-Stone C,Allan DL(2003)Phosphorus acquisition and use:critical adaptations by plants for securing a nonrenewable resource.New Phytol 157:423-447
Wu P,Ma L,Hou X,Wang M,Wu Y,Liu F,Deng XW(2003)Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves.Plant Physiol132:1260-1271
Yan W,Chen GH,Yang LF,Gai JY,Zhu YL(2014)Overexpression of the rice phosphate transporter gene OsPT6 enhances tolerance to low phosphorus stress in vegetable soybean.Sci Hortic177:71-76
Ye J,Fang L,Zheng H,Zhang Y,Chen J,Zhang Z,Wang J,Li S,Li R,Bolund L(2006)WEGO:a web tool for plotting GOannotations.Nucleic Acids Res 34:W293-W297
Benjamini Y,Yekutieli D(2001)The control of the false discovery rate in multiple testing under dependency.Ann Stat29:1165-1188
Bian L,Zheng R,Su S,Lin H,Xiao H,Wu HX,Shi J(2017)Spatial analysis increases efficiency of progeny testing of chinese fir.J For Res 28(3):445-452
Bozzo GG,Raghothama KG,Plaxton WC(2003)Purification and characterization of two secreted purple acid phosphatase isozymes from phosphate-starved tomato(Lycopersicon esculentum)cell cultures.Eur J Biochem 269:6278-6286
Chen FJ,Liu XS,Guo-Hua MI(2012)Varietal differences in plant growth,phosphorus uptake and yield formation in two maize inbred lines grown under field conditions.J Integr Agric11:1738-1743
Coelho GTCP,Carneiro NP,Karthikeyan AS,Raghothama KG,Schaffert RE,Brandao RL,Paiva LV,Souza IRP,Alves VM,Imolesi A(2010)A phosphate transporter promoter from Arabidopsis thaliana AtPHT1;4 gene drives preferential gene expression in transgenic maize roots under phosphorus starvation.Plant Mol Biol Report 28:717-723
Conesa A,Gotz S,Garc?a-Gomez JM,Terol J,Talon M,Robles M(2005)Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research.Bioinformatics21:3674-3676
Duan H,Hu D,Li Y,Zheng H(2016)Characterization of a collection of chinese fir elite genotypes using sequence-related amplified polymorphism markers.J For Res 27(5):1-6
Dubey NC,Tripathi BP,Muller M,Stamm M,Ionov L(2015)Enhanced activity of acetyl CoA synthetase adsorbed on smart microgel:an implication for precursor biosynthesis.ACS Appl Mater Interface 7:1500-1507
Fan F,Ding G,Wen X(2016)Proteomic analyses provide new insights into the responses of Pinus massoniana seedlings to phosphorus deficiency.Proteomics 16(3):504-515
Fort F,Cruz P,Stroia C,Jouany C,Catrice O,Delbrut A,Luzarreta M(2015)Root functional trait syndromes and plasticity drive the ability of grassland Fabaceae to tolerate water and phosphorus shortage.Environ Exp Bot 110:62-72
Gilbert GA,Knight JD,Vance CP,Allan DL(1999)Acid phosphatase activity in phosphorus-deficient white lupin roots.Plant Cell Environ 22(7):801-810
Guo B,Irigoyen S,Fowler TB,Versaw WK(2008)Differential expression and phylogenetic analysis suggest specialization of plastid-localized members of the PHT4 phosphate transporter family for photosynthetic and heterotrophic tissues.Plant Signal Behav 3:784-790
Hammond JP,Broadley MR,Bowen HC,Spracklen WP,Hayden RM,White PJ(2011)Gene expression changes in phosphorus deficient potato(Solanum teubrosum L.)leaves and the potential for diagnostic gene expression markers.PLoS ONE 6(9):e24606
He P,Qin H,Wu M,Wu B,Wei J,Wang D(2013)Identification of genes differentially expressed in the roots of rubber tree(Hevea brasiliensis Muell.Arg.)in response to phosphorus deficiency.Mol Biol Rep 40:1397-1405
Lapis-Gaza HR,Jost R,Finnegan PM(2014)Arabidopsis PHOS-PHATE TRANSPORTER1 genes PHT1;8 and PHT1;9 are involved in root-to-shoot translocation of orthophosphate.BMCPlant Biol 14:1-19
Li L,Liu C,Lian X(2010)Gene expression profiles in rice roots under low phosphorus stress.Plant Mol Biol 72:423-432
Li S,Ha SJ,Kim HJ,Galazka JM,Cate JHD,Jin YS,Zhao H(2013)Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization.J Biotechnol 168:1-6
Lu Yong-quan,Jia Qing,Tong Zai-kang(2014)Cloning and sequence analysis of nine novel MYB genes in Taxodiaceae plants.J For Res 25(4):795-804
Ma Z,Huang B,Xu S,Chen Y,Cao G,Ding G,Lin S(2016)Ion flux in roots of Chinese fir(Cunninghamia lanceolata(Lamb.)Hook)under aluminum stress.PLoS ONE 11:e0156832
Marschner H(1995)Mineral nutrition of higher plants,2nd edn.Academic Press,London
Miguel MA,Widrig A,Vieira RF,Brown KM,Lynch JP(2013)Basal root whorl number:a modulator of phosphorus acquisition in common bean(Phaseolus vulgaris).Ann Bot 112:973-982
Mortazavi A,Williams BA,McCue K,Schaeffer L,Wold B(2008)Mapping and quantifying mammalian transcriptomes by RNA-Seq.Nat Methods 5:621-628
Orwa C,Mutua A,Kindt R,Jamnadass R,Simons A(2015)Agroforestree database:a tree reference and selection guide version 4.0.2009.http://www.worldagroforestry.org/af/treedb/.Accessed 15 Feb 2011
Rausch C,Zimmermann P,Amrhein N,Bucher M(2004)Expression analysis suggests novel roles for the plastidic phosphate transporter Pht2;1 in auto-and heterotrophic tissues in potato and Arabidopsis.Plant J 39:13-28
Richardson AE,Lynch JP,Ryan PR,Delhaize E,Smith FA,Smith SE,Harvey PR,Ryan MH,Veneklaas EJ,Lambers H(2011)Plant and microbial strategies to improve the phosphorus efficiency of agriculture.Plant Soil 349:121-156
Rouached H,Arpat AB,Poirier Y(2010)Regulation of phosphate starvation responses in plants:signaling players and cross-talks.Mol Plant 3:288-299
Saldanha AJ(2004)Java Treeview-extensible visualization of microarray data.Bioinformatics 20:3246-3248
Sharma V,Kumar A,Archana G,Kumar GN(2016)Ensifermeliloti overexpressing Escherichia coli phytase gene(appA)improves phosphorus(P)acquisition in maize plants.Sci Nat 103:76
Simpson RJ,Oberson A,Culvenor RA,Ryan MH,Veneklaas EJ,Lambers H,Lynch JP,Ryan PR,Delhaize E,Smith FA(2011)Strategies and agronomic interventions to improve the phosphorus-use efficiency of farming systems.Plant Soil 349:89-120
Vance CP,Uhde-Stone C,Allan DL(2003)Phosphorus acquisition and use:critical adaptations by plants for securing a nonrenewable resource.New Phytol 157:423-447
Wu P,Ma L,Hou X,Wang M,Wu Y,Liu F,Deng XW(2003)Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves.Plant Physiol132:1260-1271
Yan W,Chen GH,Yang LF,Gai JY,Zhu YL(2014)Overexpression of the rice phosphate transporter gene OsPT6 enhances tolerance to low phosphorus stress in vegetable soybean.Sci Hortic177:71-76
Ye J,Fang L,Zheng H,Zhang Y,Chen J,Zhang Z,Wang J,Li S,Li R,Bolund L(2006)WEGO:a web tool for plotting GOannotations.Nucleic Acids Res 34:W293-W297