Tree Genetics & Genomes

, 13:46 | Cite as

Expression profiling in Pinus radiata infected with Fusarium circinatum

  • Angela Carrasco
  • Jill L. Wegrzyn
  • Ricardo Durán
  • Marta Fernández
  • Andrea Donoso
  • Victoria Rodriguez
  • David Neale
  • Sofía ValenzuelaEmail author
Original Article
Part of the following topical collections:
  1. Gene Expression


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.


Transcriptome 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.

Authorsʼ contributions

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.

Supplementary material

11295_2017_1125_MOESM1_ESM.docx (152 kb)
Online resource Fig. 1 Species distribution of unigene BLASTX results against the NCBI plant protein database with a cutoff E value 10−9. The twenty five plant species that gave the largest numbers of top blastx matches are shown. (DOCX 257 kb)
11295_2017_1125_MOESM2_ESM.docx (320 kb)
Online resource Fig. 2 Distribution of unique transcripts corresponding to TF gene families in P. radiata and comparison to other plant transcriptomes. The number of different encoded transcripts with the conserved DNA- binding domain of each family is represented. The distribution of TF gene families in P. taeda, P. glauca, P. abies, P. sitchensis, R.scummunis, C. clementina and V. vinifera is compared. (DOCX 319 kb)
11295_2017_1125_MOESM3_ESM.docx (316 kb)
Online resource Fig. 3 Gene ontology (GO) annotations of differentially expressed genes (DEG). Three pairwise (2, 6 and 12 dpi) comparisons of DEGs between the susceptible and the resistant genotypes of P. radiata inoculated with F. circinatum are represented. Each comparison shows the GO assignments for the up- and down-regulated genes. S: Susceptible genotype 10 at 2, 6 and 12 days post inoculation; R: Resistant genotype 1 at 2, 6 and 12 days post inoculation (DOCX 703 kb)
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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Angela Carrasco
    • 1
  • Jill L. Wegrzyn
    • 2
  • Ricardo Durán
    • 1
  • Marta Fernández
    • 1
    • 3
  • Andrea Donoso
    • 3
  • Victoria Rodriguez
    • 3
  • David Neale
    • 2
  • Sofía Valenzuela
    • 1
    • 3
    Email author
  1. 1.Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
  2. 2.Department of Plant SciencesUniversity of California DavisDavisUSA
  3. 3.Centro de BiotecnologíaUniversidad de ConcepciónConcepciónChile

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