De Novo Transcriptome Analyses of Host-fungal Interactions in Oil Palm (Elaeis Guineensis Jacq.)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2016 Jan 20

PMID 26781612

Citations 27

Authors

Chai-Ling Ho

Yung-Chie Tan

Keat-Ai Yeoh

Ahmad-Kamal Ghazali

Wai-Yan Yee

Chee-Choong Hoh

Affiliations

Soon will be listed here.

Abstract

Background: Basal stem rot (BSR) is a fungal disease in oil palm (Elaeis guineensis Jacq.) which is caused by hemibiotrophic white rot fungi belonging to the Ganoderma genus. Molecular responses of oil palm to these pathogens are not well known although this information is crucial to strategize effective measures to eradicate BSR. In order to elucidate the molecular interactions between oil palm and G. boninense and its biocontrol fungus Trichoderma harzianum, we compared the root transcriptomes of untreated oil palm seedlings with those inoculated with G. boninense and T. harzianum, respectively.

Results: Differential gene expression analyses revealed that jasmonate (JA) and salicylate (SA) may act in an antagonistic manner in affecting the hormone biosynthesis, signaling, and downstream defense responses in G. boninense-treated oil palm roots. In addition, G. boninense may compete with the host to control disease symptom through the transcriptional regulation of ethylene (ET) biosynthesis, reactive oxygen species (ROS) production and scavenging. The strengthening of host cell walls and production of pathogenesis-related proteins as well as antifungal secondary metabolites in host plants, are among the important defense mechanisms deployed by oil palm against G. boninense. Meanwhile, endophytic T. harzianum was shown to improve the of nutrition status and nutrient transportation in host plants.

Conclusion: The findings of this analysis have enhanced our understanding on the molecular interactions of G. boninense and oil palm, and also the biocontrol mechanisms involving T. harzianum, thus contributing to future formulations of better strategies for prevention and treatment of BSR.

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References

Zhou L, Cheung M, Li M, Fu Y, Sun Z, Sun S . Rice hypersensitive induced reaction protein 1 (OsHIR1) associates with plasma membrane and triggers hypersensitive cell death. BMC Plant Biol. 2011; 10:290. PMC: 3022912. DOI: 10.1186/1471-2229-10-290. View

Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P . MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004; 37(6):914-39. DOI: 10.1111/j.1365-313x.2004.02016.x. View

Veronese P, Chen X, Bluhm B, Salmeron J, Dietrich R, Mengiste T . The BOS loci of Arabidopsis are required for resistance to Botrytis cinerea infection. Plant J. 2004; 40(4):558-74. DOI: 10.1111/j.1365-313X.2004.02232.x. View

De Lorenzo G, Cervone F, Bellincampi D, Caprari C, Clark A, Desiderio A . Polygalacturonase, PGIP and oligogalacturonides in cell-cell communication. Biochem Soc Trans. 1994; 22(2):394-7. DOI: 10.1042/bst0220394. View

Schulz M, Zerbino D, Vingron M, Birney E . Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012; 28(8):1086-92. PMC: 3324515. DOI: 10.1093/bioinformatics/bts094. View

Kelleher D, Gilmore R . DAD1, the defender against apoptotic cell death, is a subunit of the mammalian oligosaccharyltransferase. Proc Natl Acad Sci U S A. 1997; 94(10):4994-9. PMC: 24619. DOI: 10.1073/pnas.94.10.4994. View

Chacon M, Rodriguez-Galan O, Benitez T, Sousa S, Rey M, Llobell A . Microscopic and transcriptome analyses of early colonization of tomato roots by Trichoderma harzianum. Int Microbiol. 2007; 10(1):19-27. View

Zerbino D, Birney E . Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18(5):821-9. PMC: 2336801. DOI: 10.1101/gr.074492.107. View

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D . Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. PMC: 2752132. DOI: 10.1101/gr.092759.109. View

10.

Ariani A, Di Baccio D, Romeo S, Lombardi L, Andreucci A, Lux A . RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc. PLoS One. 2015; 10(2):e0117571. PMC: 4324836. DOI: 10.1371/journal.pone.0117571. View

11.

Anders S, Huber W . Differential expression analysis for sequence count data. Genome Biol. 2010; 11(10):R106. PMC: 3218662. DOI: 10.1186/gb-2010-11-10-r106. View

12.

Lochman J, Mikes V . Ergosterol treatment leads to the expression of a specific set of defence-related genes in tobacco. Plant Mol Biol. 2006; 62(1-2):43-51. DOI: 10.1007/s11103-006-9002-5. View

13.

Trapnell C, Pachter L, Salzberg S . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. PMC: 2672628. DOI: 10.1093/bioinformatics/btp120. View

14.

Mittler R . Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002; 7(9):405-10. DOI: 10.1016/s1360-1385(02)02312-9. View

15.

Harman G, Howell C, Viterbo A, Chet I, Lorito M . Trichoderma species--opportunistic, avirulent plant symbionts. Nat Rev Microbiol. 2004; 2(1):43-56. DOI: 10.1038/nrmicro797. View

16.

Wang T, Zhang N, Du L . Isolation of RNA of high quality and yield from Ginkgo biloba leaves. Biotechnol Lett. 2005; 27(9):629-33. DOI: 10.1007/s10529-005-3629-1. View

17.

Ye M, Chen Z, Su X, Ji L, Wang J, Liao W . Study of seed hair growth in Populus tomentosa, an important character of female floral bud development. BMC Genomics. 2014; 15:475. PMC: 4089023. DOI: 10.1186/1471-2164-15-475. View

18.

Contreras-Cornejo H, Macias-Rodriguez L, Beltran-Pena E, Herrera-Estrella A, Lopez-Bucio J . Trichoderma-induced plant immunity likely involves both hormonal- and camalexin-dependent mechanisms in Arabidopsis thaliana and confers resistance against necrotrophic fungi Botrytis cinerea. Plant Signal Behav. 2011; 6(10):1554-63. PMC: 3256384. DOI: 10.4161/psb.6.10.17443. View

19.

Kersten P, Cullen D . Copper radical oxidases and related extracellular oxidoreductases of wood-decay Agaricomycetes. Fungal Genet Biol. 2014; 72:124-130. DOI: 10.1016/j.fgb.2014.05.011. View

20.

Wang K, Li H, Ecker J . Ethylene biosynthesis and signaling networks. Plant Cell. 2002; 14 Suppl:S131-51. PMC: 151252. DOI: 10.1105/tpc.001768. View