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De novo transcriptome analysis of Fraxinus velutina Torr in response to NaCl stress

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Abstract

This study aimed to further clarify the mechanisms of salt-alkali tolerance in Fraxinus velutina Torr. Shoots obtained from Fraxinus velutina Torr (also known as velvet ash or Arizona ash) and of Fraxinus chinensis Roxb (controls) were planted in a greenhouse with hydroponics and 1-year-old seedlings were irrigated with 40 mM NaCl, followed by 80 mM NaCl; young leaves were then harvested and sequenced from total RNA. Differential expression gene analyses of Fraxinus velutina Torr as well as that of Fraxinus chinensis Roxb before and after treatment were conducted. The Gene Ontology biological process (GO-BP) terms and pathways enriched by overlapping genes were analyzed, and the co-expression network of them was built. A total of 454 overlapping upregulated and 278 overlapping downregulated genes were found in the two comparisons. Upregulated genes were mainly enriched in GO-BP terms of alkaloid biosynthetic process, and the pathways such as Ras signaling pathway, while downregulated genes were primarily enriched in photosynthesis and phenylpropanoid biosynthesis. The processes of phenylpropanoid biosynthesis and photosynthesis, as well as metallothionein-like protein and photosystem I P700–related proteins, appear to be involved in salt stress tolerance in Fraxinus velutina Torr.

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References

  • Abdallah SB, Aung B, Amyot L, Lalin I, Lachâal M, Karray-Bouraoui N, Hannoufa A (2016) Salt stress (NaCl) affects plant growth and branch pathways of carotenoid and flavonoid biosyntheses in Solanum nigrum. Acta Physiol Plant 38:1–13

    Article  Google Scholar 

  • Agati G, Biricolti S, Guidi L, Ferrini F, Fini A, Tattini M (2011) The biosynthesis of flavonoids is enhanced similarly by UV radiation and root zone salinity in L. vulgare leaves. J Plant Physiol 168:204–212

    Article  CAS  Google Scholar 

  • Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. Bmc Bioinformatics 4:2

    Article  Google Scholar 

  • Baxter HL, Jr CNS (2013) Effects of altered lignin biosynthesis on phenylpropanoid metabolism and plant stress. Biofuels 4:635–650

    Article  CAS  Google Scholar 

  • Benjamini Y, Hochberg Y (2009) Controlling the false discovery rate : a practical and powerful approach to multiple testing author (s ): Yoav Benjamini and Yosef Hochberg source : J R Stat Soc Ser B ( Methodol ), Vol . 57 , No. 1 Published by

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  • Chen C, Song Y, Zhuang K, Li L, Xia Y, Shen Z (2015) Proteomic analysis of copper-binding proteins in excess copper-stressed roots of two rice (Oryza sativa L.) varieties with different Cu tolerances. PLoS One 10:e0125367

    Article  Google Scholar 

  • Du ZY, Wang QH, Xing SJ, Liu FC, Ma BY, Ma HL, Liu DX (2015) Fine root distribution, characteristics and rhizosphere soil properties in a mixed stand of Robinia pseudoacacia and Fraxinus velutina in a saline soil. @ 47

  • Farnworth P, Hillcoat B, Roos I (1990) Metallothionein-like proteins and cell resistance to cis -dichlorodiammineplatinum(II) in L1210 cells. Cancer Chemother Pharmacol 25:411–417

    Article  CAS  Google Scholar 

  • Fornalé S, Shi X, Chai C, Encina A, Irar S, Capellades M, Fuguet E, Torres JL, Rovira P, Puigdomènech P, Rigau J, Grotewold E, Gray J, Caparrós-Ruiz D (2010) ZmMYB31 directly represses maize lignin genes and redirects the phenylpropanoid metabolic flux. Plant J Cell Mol Biol 64:633–644

    Article  Google Scholar 

  • Gil R et al. (2014) Responses of five Mediterranean halophytes to seasonal changes in environmental conditions AoB PLANTS,6,2016(2014-8-19) 6:655–676

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29:644–652

    Article  CAS  Google Scholar 

  • Kalaji HM, Cetner MD, Samborska IA, Lukasik I, Oukarroum A, Rusinowski S, Pietkiewicz S, Świątek M, Dąbrowski P (2016) Effective microorganisms impact on photosynthetic activity of Arabidopsis plant grown under salinity stress conditions. Ann Warsaw Univ Life Sci– Sggw Land Reclamation 48:153–163

    Article  Google Scholar 

  • Kanehisa M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:480–484

    Article  Google Scholar 

  • Kim BG, Waadt R, Cheong YH, Pandey GK, Dominguez-Solis JR, Schültke S, Lee SC, Kudla J, Luan S (2007) The calcium sensor CBL10 mediates salt tolerance by regulating ion homeostasis in Arabidopsis. Plant J Cell Mol Biol 52:473–484

    Article  CAS  Google Scholar 

  • Lee SH, Zwiazek JJ (2018) Water transport properties of root cells contribute to salt tolerance in halophytic grasses Poa juncifolia and Puccinellia nuttalliana. A Vaziriyeganeh M Plant science :Int J Exp Plant Biol 276:54–62

    Google Scholar 

  • Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Bmc Bioinformatics 12:323

    Article  CAS  Google Scholar 

  • Li SJ, Zhan YG, Yang CP, Wu ZP, Ren L, Xu XY, Ge SJ (2010) Effects on growth and physiological indices of introduced species of Fraxinus velutina under mixed salt stress. Journal of Northeast Forestry University 38:15–17

    Google Scholar 

  • Li Y et al (2018) Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance. %A Zhang J BMC Plant Biol 18:124

    Article  Google Scholar 

  • Mao P et al. (2017) Eco-physiological adaptability in mixtures of Robinia pseudoacacia and Fraxinus velutina and coastal eco-engineering

  • Maury S, Delaunay A, Mesnard F, Crônier D, Chabbert B, Geoffroy P, Legrand M (2010) O-methyltransferase(s)-suppressed plants produce lower amounts of phenolic vir inducers and are less susceptible to Agrobacterium tumefaciens infection. Planta 232:975–986

    Article  CAS  Google Scholar 

  • Mishra A, Sharma SD, Khan GH (2003) Improvement in physical and chemical properties of sodic soil by 3, 6 and 9 years old plantation of Eucalyptus tereticornis.Nat. Methods 184:115–124

    Google Scholar 

  • Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  Google Scholar 

  • Negrão S, Schmöckel SM, Tester M (2016) Evaluating physiological responses of plants to salinity stress. Ann Bot 119:1–11

    Article  Google Scholar 

  • Nishiuchi S, Liu S, Takano T (2007) Isolation and characterization of a metallothionein-1 protein in Chloris virgata Swartz that enhances stress tolerances to oxidative, salinity and carbonate stress in Saccharomyces cerevisiae. Biotechnol Lett 29:1301–1305

    Article  CAS  Google Scholar 

  • Ping L (2010) Seed germination characteristics of Fraxinus velutina Torr in treatments with salt extract of saline soil Journal of Anhui Agricultural Sciences

  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

    Article  CAS  Google Scholar 

  • Shao T, Li L, Wu Y, Chen M, Long X, Shao H, Liu Z, Rengel Z (2016) Balance between salt stress and endogenous hormones influence dry matter accumulation in Jerusalem artichoke. Sci Total Environ 568:891–898

    Article  CAS  Google Scholar 

  • Shinae M, Youngjoon K, Gyubum K, Kwangwoo J, Floyd A, Heitman J, Yongsun B (2010) Comparative transcriptome analysis reveals novel roles of the Ras and cyclic AMP signaling pathways in environmental stress response and antifungal drug sensitivity in Cryptococcus neoformans. Eukaryot Cell 9:360–378

    Article  Google Scholar 

  • Stein H, Honig A, Miller G, Erster O, Eilenberg H, Csonka LN, Szabados L, Koncz C, Zilberstein A (2011) Elevation of free proline and proline-rich protein levels by simultaneous manipulations of proline biosynthesis and degradation in plants. Plant Sci 181:140–150

    Article  CAS  Google Scholar 

  • Sudhir P, Murthy SDS (2004) Effects of salt stress on basic processes of photosynthesis. Photosynthetica 42:481–486

    Article  CAS  Google Scholar 

  • Szabados L, Savouré A (2010) Proline: a multifunctional amino acid. Trends Plant Sci 15:89–97

    Article  CAS  Google Scholar 

  • Tarazona S, Furió-Tarí P, Turrà D, Pietro AD, Nueda MJ, Ferrer A, Conesa A (2015) Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package. Nucleic Acids Res 43:e140

    PubMed  PubMed Central  Google Scholar 

  • Wang Y, Zhao Z, Zhang L, Hu C, Ren C, Yuan L (2014) Molecular characterization of metallothionein from white shrimp, Litopenaeus vannamei and its expression response to salinity stress. Mar Biol Res 10:731–737

    Article  Google Scholar 

  • Wu M, Cao B (2006) Studies on germination and physiological characteristics of Fraxinus velutina seeds from salt and Normal soils seed

  • Yao Y (2012) Fraxinus velutina Torr. afforestation techniques on the saline-alkali soil. Ningxia Journal of Agriculture & Forestry Science & Technology

  • Zhang XJ, Chen TT, Song XY, Zheng H, Fan SJ (2009) Antimicrobial activity of the extracts from Fraxinus velutina Torr fruits. Acta Botan Boreali-Occiden Sin:824–828

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Funding

This work was supported by Research on Molecular Evaluation of Germplasm Resources and Development of Embryo Freezing Technology of Fraxinus L. (Project No. 2014GNC111006) and the Study on Germplasm Resources Exploration, Innovation and Utilization of Forest Tree Species (Project No. 2013BA001B06).

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Author notes

  1. Liping Yan and Cuilan Liu contributed equally to this work.

Authors and Affiliations

  1. Shandong Provincial Academy of Forestry, No. 42 East Wenhua Road, Jinan, 250014, Shandong, China

    Liping Yan, Cuilan Liu, Yinhua Wang, Kaifang Wang, Fei Ren, Junxiu Yao & Dejun Wu

  2. Shandong Provincial Key Laboratory of Forest Tree Genetic Improvement, Jinan, 250014, Shandong, China

    Liping Yan, Cuilan Liu, Yinhua Wang, Kaifang Wang, Fei Ren, Junxiu Yao & Dejun Wu

Authors
  1. Liping Yan
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  2. Cuilan Liu
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  3. Yinhua Wang
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  4. Kaifang Wang
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  7. Dejun Wu
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Correspondence to Dejun Wu.

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Communicated by C. Kulheim

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Supplementary fig. 1

The co-expression network of upregulated differentially expressed genes (DEGs). The nodes are the genes, and the edges indicate the interaction between nodes. (PNG 669 kb)

High Resolution Image (TIF 1794 kb)

Supplementary fig. 2

The co-expression network of downregulated differentially expressed genes (DEGs). The nodes are the genes, and the edges indicate the interaction between nodes. (PNG 756 kb)

High Resolution Image (TIF 2224 kb)

Data archiving statement

The sequencing results have been uploaded to the National Center for Biotechnology Information (NCBI) under the accession number SSR1037160.

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Yan, L., Liu, C., Wang, Y. et al. De novo transcriptome analysis of Fraxinus velutina Torr in response to NaCl stress. Tree Genetics & Genomes 15, 56 (2019). https://doi.org/10.1007/s11295-019-1340-y

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  • DOI: https://doi.org/10.1007/s11295-019-1340-y

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