Molecular Genetics and Genomics

, Volume 290, Issue 5, pp 1963–1977 | Cite as

Transcriptomic profiles of the smoke tree wilt fungus Verticillium dahliae under nutrient starvation stresses

  • Dianguang Xiong
  • Yonglin WangEmail author
  • Chengming Tian
Original Paper


Verticillium dahliae is a notorious plant pathogen that causes vascular wilt on more than 200 plant species. During plant infection, efficient pathogen nutrition during the interaction with the host is a requisite for successful infection. However, little attention has been focused on nutrient uptake and starvation responses in this fungus. Here, we used RNA-Seq to analyze the response of V. dahliae to nutrient starvation, including carbon and nitrogen depletion. Gene expression profile analysis showed that 1854 genes were differentially expressed under carbon starvation (852 upregulated and 539 downregulated genes) and nitrogen starvation (487 upregulated and 291 downregulated genes). Among the differentially expressed genes, genes involved in utilization or production acetyl-CoA, including glycolysis, fatty acid biosynthesis or metabolism, and melanin biosynthesis, were repressed under carbon starvation, whereas melanin biosynthesis genes were strongly induced under nitrogen starvation. These results, combined with VDH1 expression data, suggested that melanin biosynthesis and microsclerotia development were induced under nitrogen starvation, but microsclerotia development was suppressed under carbon starvation. Furthermore, many genes encoding carbohydrate-active enzymes and secreted proteins were induced under carbon starvation. Overall, the results improve our understanding of the response of V. dahliae to nutrient starvation and help to identify potential virulence factors for the development of novel disease control strategies.


Verticillium dahliae Nutrient starvation Melanin biosynthesis Carbohydrate-active enzymes 



The research was funded by Beijing Higher Education Young Elite Teacher Project (YETP0737), the National Natural Science Foundation of China (31370013), and the Fundamental Research Funds for the Central Universities (BLYJ201507).

Conflict of interest

The authors declare that they have no competing interests.

Compliance with ethical standards

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

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Supplementary material 5 (TIFF 5655 kb) Additional file 5: Fig. S1 Validation of the digital gene expression (DGE) patterns. The expression patterns obtained by qRT-PCR analysis for the selected genes were similar to those obtained by DGE analysis
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Supplementary material 6 (TIFF 14581 kb) Additional file 6: Fig. S2 Differences in microsclerotia formation under different incubation conditions. (a) Macro- and micro-view of microsclerotia formation under BM, BM-C, and BM-N after incubation for an additional 2 days with 150 rpm shaking (as described in the Materials and methods). (b) Macro- and micro-view of microsclerotia formation under BM, BM-C, and BM-N after incubation for an additional 2 days with stationary culture. In order to photograph the cultures, about 1.5 ml culture solution was sampled and centrifuged
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Supplementary material 7 (TIFF 6791 kb) Additional file 7: Fig. S3 Differences in microsclerotia formation under different incubation conditions after culture for 20 days. (a) Macro-view of microsclerotia formation under BM-C and BM-N after incubation for an additional 20 days with 150 rpm shaking (as described in the Materials and methods). (b) Macro-view of microsclerotia formation under BM-C and BM-N after incubation for an additional 20 days with stationary culture. In order to photograph the cultures, about 1 ml culture solution was sampled and centrifuged


  1. Alves SL, Herberts RA, Hollatz C, Trichez D, Miletti LC, de Araujo PS, Stambuk BU (2008) Molecular analysis of maltotriose active transport and fermentation by Saccharomyces cerevisiae reveals a determinant role for the AGT1 permease. Appl Environ Microbiol 74:1494–1501PubMedCentralCrossRefPubMedGoogle Scholar
  2. Amselem J, Cuomo CA, van Kan JA, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quevillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collemare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Guldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuveglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Segurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7:e1002230PubMedCentralCrossRefPubMedGoogle Scholar
  3. Andersen PC, Brodbeck BV (1989) Diurnal and temporal changes in the chemical profile of xylem exudate from Vitis rotundifolia. Physiol Plant 75:63–70CrossRefGoogle Scholar
  4. Bailey C, Arst HN (1975) Carbon catabolite repression in Aspergillus nidulans. Eur J Biochem 51:573–577CrossRefPubMedGoogle Scholar
  5. Bailey A, Mueller E, Bowyer P (2000) Ornithine decarboxylase of Stagonospora (Septoria) nodorum is required for virulence toward wheat. J Biol Chem 275:14242–14247CrossRefPubMedGoogle Scholar
  6. Benz JP, Chau BH, Zheng D, Bauer S, Glass NL, Somerville CR (2014) A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations. Mol Microbiol 91:275–299PubMedCentralCrossRefPubMedGoogle Scholar
  7. Bhat RG, Subbarao KV (1999) Host Range Specificity in Verticillium dahliae. Phytopathology 89:1218–1225CrossRefPubMedGoogle Scholar
  8. Bidochka MJ, Burke S, Ng L (1999) Extracellular hydrolytic enzymes in the fungal genus Verticillium: adaptations for pathogenesis. Can J Microbiol 45:856–864CrossRefGoogle Scholar
  9. Bishop CD, Cooper RM (1984) Ultrastructure of vascular colonization by fungal wilt pathogens. II. Invasion of resistant cultivars. Physiol Plant Pathol 24:277–289CrossRefGoogle Scholar
  10. Coleman M, Henricot B, Arnau J, Oliver RP (1997) Starvation-induced genes of the tomato pathogen Cladosporium fulvum are also induced during growth in planta. Mol Plant Microbe Interact 10:1106–1109CrossRefPubMedGoogle Scholar
  11. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefPubMedGoogle Scholar
  12. Coradetti ST, Craig JP, Xiong Y, Shock T, Tian C, Glass NL (2012) Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi. Proc Natl Acad Sci USA 109:7397–7402PubMedCentralCrossRefPubMedGoogle Scholar
  13. Coradetti ST, Xiong Y, Glass NL (2013) Analysis of a conserved cellulase transcriptional regulator reveals inducer-independent production of cellulolytic enzymes in Neurospora crassa. Microbiologyopen 2:595–609PubMedCentralCrossRefPubMedGoogle Scholar
  14. Cresnar B, Petric S (2011) Cytochrome P450 enzymes in the fungal kingdom. Biochim Biophys Acta 1814:29–35CrossRefPubMedGoogle Scholar
  15. de Souza WR, de Gouvea PF, Savoldi M, Malavazi I, de Souza Bernardes LA, Goldman MH, de Vries RP, de Castro Oliveira JV, Goldman GH (2011) Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse. Biotechnol Biofuels 4:40PubMedCentralCrossRefPubMedGoogle Scholar
  16. Decottignies A, Goffeau A (1997) Complete inventory of the yeast ABC proteins. Nat Genet 15:137–145CrossRefPubMedGoogle Scholar
  17. Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA, Archer DB (2012) Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet 8:e1002875PubMedCentralCrossRefPubMedGoogle Scholar
  18. Dimond AE (1970) Biophysics and biochemistry of the vascular wilt syndrome. Annu Rev Phytopathol 8:301–322CrossRefGoogle Scholar
  19. Divon HH, Fluhr R (2007) Nutrition acquisition strategies during fungal infection of plants. FEMS Microbiol Lett 266:65–74CrossRefPubMedGoogle Scholar
  20. Dixon GR, Pegg GF (1972) Changes in amino-acid content of tomato xylem sap following infection with strains of Verticillium albo-atrum. Ann Bot 36:147–154Google Scholar
  21. Dobinson KF, Lecomte N, Lazarovits G (1997) Production of an extracellular trypsin-like protease by the fungal plant pathogen Verticillium dahliae. Can J Microbiol 43:227–233CrossRefPubMedGoogle Scholar
  22. Dobinson KF, Grant SJ, Kang S (2004) Cloning and targeted disruption, via Agrobacterium tumefaciens-mediated transformation, of a trypsin protease gene from the vascular wilt fungus Verticillium dahliae. Curr Genet 45:104–110CrossRefPubMedGoogle Scholar
  23. Dowzer CE, Kelly JM (1991) Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans. Mol Cell Biol 11:5701–5709PubMedCentralPubMedGoogle Scholar
  24. Duressa D, Anchieta A, Chen D, Klimes A, Garcia-Pedrajas MD, Dobinson KF, Klosterman SJ (2013) RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae. BMC Genom 14:607CrossRefGoogle Scholar
  25. Faino L, de Jonge R, Thomma BP (2012) The transcriptome of Verticillium dahliae-infected Nicotiana benthamiana determined by deep RNA sequencing. Plant Signal Behav 7:1065–1069PubMedCentralCrossRefPubMedGoogle Scholar
  26. Fernandez J, Wright JD, Hartline D, Quispe CF, Madayiputhiya N, Wilson RA (2012) Principles of carbon catabolite repression in the rice blast fungus: Tps1, Nmr1-3, and a MATE-family pump regulate glucose metabolism during infection. PLoS Genet 8:e1002673PubMedCentralCrossRefPubMedGoogle Scholar
  27. Garas NA, Wilhem S, Sagen JE (1986) Relationship of cultivar resistance to distribution of Verticillium dahliae in inoculated cotton plants and to growth of single conidia on excised stem segments. Phytopathology 76:1005–1010CrossRefGoogle Scholar
  28. Glass NL, Schmoll M, Cate JH, Coradetti S (2013) Plant cell wall deconstruction by ascomycete fungi. Annu Rev Microbiol 67:477–498CrossRefPubMedGoogle Scholar
  29. Jiang C, Zhang S, Zhang Q, Tao Y, Wang C, Xu JR (2015) FgSKN7 and FgATF1 have overlapping functions in ascosporogenesis, pathogenesis and stress responses in Fusarium graminearum. Environ Microbiol 17:1245–1260CrossRefPubMedGoogle Scholar
  30. Klimes A, Dobinson KF (2006) A hydrophobin gene, VDH1, is involved in microsclerotial development and spore viability in the plant pathogen Verticillium dahliae. Fungal Genet Biol 43:283–294CrossRefPubMedGoogle Scholar
  31. Klimes A, Amyotte SG, Grant S, Kang S, Dobinson KF (2008) Microsclerotia development in Verticillium dahliae: regulation and differential expression of the hydrophobin gene VDH1. Fungal Genet Biol 45:1525–1532CrossRefPubMedGoogle Scholar
  32. Klosterman SJ, Atallah ZK, Vallad GE, Subbarao KV (2009) Diversity, pathogenicity, and management of verticillium species. Annu Rev Phytopathol 47:39–62CrossRefPubMedGoogle Scholar
  33. Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma LJ (2011) Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog 7:e1002137PubMedCentralCrossRefPubMedGoogle Scholar
  34. Krems B, Charizanis C, Entian KD (1996) The response regulator-like protein Pos9/Skn7 of Saccharomyces cerevisiae is involved in oxidative stress resistance. Curr Genet 29:327–334CrossRefPubMedGoogle Scholar
  35. Marzluf GA (1997) Genetic regulation of nitrogen metabolism in the fungi. Microbiol Mol Biol Rev 61:17–32PubMedCentralPubMedGoogle Scholar
  36. Neumann MJ, Dobinson KF (2003) Sequence tag analysis of gene expression during pathogenic growth and microsclerotia development in the vascular wilt pathogen Verticillium dahliae. Fungal Genet Biol 38:54–62CrossRefPubMedGoogle Scholar
  37. Ozcan S, Johnston M (1995) Three different regulatory mechanisms enable yeast hexose transporter (HXT) genes to be induced by different levels of glucose. Mol Cell Biol 15:1564–1572PubMedCentralPubMedGoogle Scholar
  38. Ozcan S, Johnston M (1999) Function and regulation of yeast hexose transporters. Microbiol Mol Biol Rev 63:554–569PubMedCentralPubMedGoogle Scholar
  39. Rauyaree P, Ospina-Giraldo MD, Kang S, Bhat RG, Subbarao KV, Grant SJ, Dobinson KF (2005) Mutations in VMK1, a mitogen-activated protein kinase gene, affect microsclerotia formation and pathogenicity in Verticillium dahliae. Curr Genet 48:109–116CrossRefPubMedGoogle Scholar
  40. Rioux D, Nicole M, Simard M, Ouellette GB (1998) Immunocytochemical evidence that secretion of pectin occurs during gel (gum) and tylosis formation in trees. Phytopathology 88:494–505CrossRefPubMedGoogle Scholar
  41. Santhanam P, van Esse HP, Albert I, Faino L, Nurnberger T, Thomma BPHJ (2013) Evidence for functional diversification within a fungal NEP1-Like protein family. Mol Plant Microbe Interact 26:278–286CrossRefPubMedGoogle Scholar
  42. Snoeijers SS, Pérez-García A, Joosten MH, De Wit PJ (2000) The effect of nitrogen on disease development and gene expression in bacterial and fungal plant pathogens. Eur J Plant Pathol 106:493–506CrossRefGoogle Scholar
  43. Soanes DM, Chakrabarti A, Paszkiewicz KH, Dawe AL, Talbot NJ (2012) Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae. PLoS Pathog 8:e1002514PubMedCentralCrossRefPubMedGoogle Scholar
  44. Solomon PS, Thomas SW, Spanu P, Oliver RP (2003) The utilisation of di/tripeptides by Stagonospora nodorum is dispensable for wheat infection. Physiol Mol Plant Pathol 63:191–199CrossRefGoogle Scholar
  45. Staples RC (2000) Research on the rust fungi during the twentieth century. Annu Rev Phytopathol 38:49–69CrossRefPubMedGoogle Scholar
  46. Talbot NJ, Ebbole DJ, Hamer JE (1993) Identification and characterization of MPG1, a gene involved in pathogenicity from the rice blast fungus Magnaporthe grisea. Plant Cell 5:1575–1590PubMedCentralCrossRefPubMedGoogle Scholar
  47. Thevelein JM (1984) Regulation of trehalose mobilization in fungi. Microbiol Rev 48:42–59PubMedCentralPubMedGoogle Scholar
  48. Thines E, Weber RW, Talbot NJ (2000) MAP kinase and protein kinase A-dependent mobilization of triacylglycerol and glycogen during appressorium turgor generation by Magnaporthe grisea. Plant Cell 12:1703–1718PubMedCentralPubMedGoogle Scholar
  49. Thomas SW, Rasmussen SW, Glaring MA, Rouster JA, Christiansen SK, Oliver RP (2001) Gene identification in the obligate fungal pathogen Blumeria graminis by expressed sequence tag analysis. Fungal Genet Biol 33:195–211CrossRefPubMedGoogle Scholar
  50. Tran VT, Braus-Stromeyer SA, Kusch H, Reusche M, Kaever A, Kuhn A, Valerius O, Landesfeind M, Asshauer K, Tech M, Hoff K, Pena-Centeno T, Stanke M, Lipka V, Braus GH (2014) Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots. New Phytol 202:565–581CrossRefPubMedGoogle Scholar
  51. Tzima AK, Paplomatas EJ, Tsitsigiannis DI, Kang S (2012) The G protein beta subunit controls virulence and multiple growth- and development-related traits in Verticillium dahliae. Fungal Genet Biol 49:271–283CrossRefPubMedGoogle Scholar
  52. van Munster JM, Daly P, Delmas S, Pullan ST, Blythe MJ, Malla S, Kokolski M, Noltorp EC, Wennberg K, Fetherston R, Beniston R, Yu X, Dupree P, Archer DB (2014) The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. Fungal Genet Biol 72:34–47PubMedCentralCrossRefPubMedGoogle Scholar
  53. Wang YL, Xiao SX, Xiong DG, Tian CM (2013) Genetic transformation, infection process and qPCR quantification of Verticillium dahliae on smoke-tree Cotinus coggygria. Australas Plant Pathol 42:33–41CrossRefGoogle Scholar
  54. Wilhelm S (1955) Longevity of the Verticillium wilt fungus in the laboratory and field. Phytopathology 45:180–181Google Scholar
  55. Wilson RA, Arst HN (1998) Mutational analysis of AREA, a transcriptional activator mediating nitrogen metabolite repression in Aspergillus nidulans and a member of the “streetwise” GATA family of transcription factors. Microbiol Mol Biol Rev 62:586–596PubMedCentralPubMedGoogle Scholar
  56. Wilson RA, Fernandez J, Quispe CF, Gradnigo J, Seng A, Moriyama E, Wright JD (2012) Towards defining nutrient conditions encountered by the rice blast fungus during host infection. PLoS One 7:e47392PubMedCentralCrossRefPubMedGoogle Scholar
  57. Wood RKS (1961) Verticillium wilt of tomatoes—the role of pectic and cellulolytic enzymes. Ann Appl Biol 49:120–139CrossRefGoogle Scholar
  58. Xiong D, Wang Y, Ma J, Klosterman SJ, Xiao S, Tian C (2014) Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae. BMC Genomics 15:324PubMedCentralCrossRefPubMedGoogle Scholar
  59. Yi M, Valent B (2013) Communication between filamentous pathogens and plants at the biotrophic interface. Annu Rev Phytopathol 51:587–611CrossRefPubMedGoogle Scholar
  60. Znameroski EA, Glass NL (2013) Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction. Biotechnol Biofuels 6:1–8CrossRefGoogle Scholar
  61. Znameroski EA, Coradetti ST, Roche CM, Tsai JC, Iavarone AT, Cate JH, Glass NL (2012) Induction of lignocellulose-degrading enzymes in Neurospora crassa by cellodextrins. Proc Natl Acad Sci USA 109:6012–6017PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of ForestryBeijing Forestry UniversityBeijingChina

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