Expression profiling in Pinus radiata infected with Fusarium circinatum
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Fusarium circinatum is the causal agent of pitch canker, a serious disease that affects numerous Pinus species worldwide. Pinus species have varying degrees of susceptibility to this pathogen, being Pinus radiata one of the most susceptible species. Quantitative phenotypic variation and intermediate heritability in response to F. circinatum have been observed by studies of controlled inoculations in several families of P. radiata, suggesting the existence of a genetic component to resistance. Recent experiments in conifer genomics have identified several genes with functions that confer resistance to various biotic and abiotic stresses. In this investigation, high-throughput mRNA sequencing (RNA-seq) is used to identify differentially expressed genes during the interaction of P. radiata with F. circinatum at several time points including uninfected plants at 2, 6, and 12 days post inoculation (dpi) in two contrasting genotypes. The 470,612 Roche 454-HQ reads were de novo assembled into a transcriptome containing 26,215 unigenes with an average length of 1523 bp. Functional annotation indicated that 86% had significant protein alignments and 23,897 (91%) could be assigned to one or more Gene Ontology (GO) terms. Pairwise comparisons of the differentially expressed genes, up and downregulated between the inoculated genotypes, wounded and unwounded control for the resistant genotype at time 2, 6 and 12 dpi were performed. A total of 39,242 and 51 commonly upregulated genes in response to pitch canker infection at 2, 6, and 12 dpi, respectively, during three pairwise comparisons were identified. This RNA-seq analysis identified a total of 293 putative candidate genes and validated a set of genes involved in cellular processes and defense mechanisms, among them, 32 upregulated genes have been associated with defense response in plants against pathogens, thereby providing the first comprehensive evaluation of the putative mechanisms of F. circinatum resistance in pine.
KeywordsTranscriptome RNA-seq Differential expression genes Pathogen Defense genes
This work was financed by the Genómica Forestal SA and CORFO Grant 12FBCT-16466. We would like to thank CONICYT doctoral scholarship N° 21090780 (AC) and Hans Vasquez-Grozz for bioinformatics support.
AC performed the transcriptome study, analyzed the DEG results, statistical analysis, and wrote main part of the manuscript. AC, AD, and VR performed the inoculation experiments and qRT-PCR analysis. AC and JW assembled and annotated the 454-transcriptome. AC and SV designed the 454 and Illumina library construction, provided advice and oversight on sequencing. MF, RD, and DN helped with the bioinformatics analysis and strategies. SV is the PI of the research. All authors have edited, read, and approved the final version of the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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