Skip to main content
SpringerLink
Log in

Expression profiling in Pinus radiata infected with Fusarium circinatum

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Adie BA, Perez-Perez J, Perez-Perez MM, Godoy M, Sanchez-Serrano JJ, Schmelz EA, Solano R (2007) ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis. Plant Cell 19:1665–1681. doi:10.1105/tpc.106.048041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Adomas A et al (2007) Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion. Tree Physiol 27:1441–1458

    Article  CAS  PubMed  Google Scholar 

  • Asiegbu FO, Nahalkova J, Li G (2005) Pathogen-inducible cDNAs from the interaction of the root rot fungus Heterobasidion annosum with scots pine (Pinus sylvestris L.) Plant Sci 168:365–372. doi:10.1016/j.plantsci.2004.08.010

    Article  CAS  Google Scholar 

  • Azaiez A, Boyle B, Levee V, Seguin A (2009) Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi. Molecular plant-microbe interactions: MPMI 22:190–200. doi:10.1094/MPMI-22-2-0190

    Article  CAS  PubMed  Google Scholar 

  • Barakat A et al (2009) Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection. BMC Plant Biol 9:51. doi:10.1186/1471-2229-9-51

    Article  PubMed  PubMed Central  Google Scholar 

  • Barakat A et al (2012) Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biol 12:38. doi:10.1186/1471-2229-12-38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blodgett JT, Eyles A, Bonello P (2007) Organ-dependent induction of systemic resistance and systemic susceptibility in Pinus nigra inoculated with Sphaeropsis sapinea and Diplodia scrobiculata. Tree Physiol 27:511–517

  • Bonello P, Blodgett JT (2003) Pinus nigra–Sphaeropsis sapinea as a model pathosystem to investigate local and systemic effects of fungal infection of pines. Physiol Mol Plant Pathol 63:249–261. doi:10.1016/j.pmpp.2004.02.002

    Article  Google Scholar 

  • Bonello P, Gordon TR, Storer AJ (2001) Systemic induced resistance in Monterey pine. For Pathol 31:99–106

  • Canales J et al (2014) De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnol J 12:286–299. doi:10.1111/pbi.12136

    Article  CAS  PubMed  Google Scholar 

  • Cañas RA, Feito I, Fuente-Maqueda JF, Avila C, Majada J, Canovas FM (2015) Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats. BMC Genomics 16:909. doi:10.1186/s12864-015-2177-x

    Article  PubMed  PubMed Central  Google Scholar 

  • Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116. doi:10.1007/BF02670468

    Article  CAS  Google Scholar 

  • Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159. doi:10.1101/gr.1917404

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cook DC, Matheson AC (2008) An estimate of the potential economic impact of pine pitch canker in Australia. Aust For 71:107–112

    Article  Google Scholar 

  • Coppinger P, Repetti PP, Day B, Dahlbeck D, Mehlert A, Staskawicz BJ (2004) Overexpression of the plasma membrane-localized NDR1 protein results in enhanced bacterial disease resistance in Arabidopsis thaliana. The Plant journal : for cell and molecular biology 40:225–237. doi:10.1111/j.1365-313X.2004.02203.x

    Article  CAS  Google Scholar 

  • Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC bioinformatics 11:485. doi:10.1186/1471-2105-11-485

    Article  PubMed  PubMed Central  Google Scholar 

  • Donoso A, Rodriguez V, Carrasco A, Ahumada R, Sanfuentes E, Valenzuela S (2015) Relative expression of seven candidate genes for pathogen resistance on Pinus radiata infected with Fusarium circinatum. Physiol Mol Plant Pathol. doi:10.1016/j.pmpp.2015.08.009

    Google Scholar 

  • Duplessis S, Major I, Martin F, Séguin A (2009) Poplar and pathogen interactions: insights from populus genome-wide analyses of resistance and defense gene families and gene expression profiling. Crit Rev Plant Sci 28:309–334. doi:10.1080/07352680903241063

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. doi:10.1093/bioinformatics/btq461

    Article  CAS  PubMed  Google Scholar 

  • Fernandez-Pozo N et al (2011) EuroPineDB: a high-coverage web database for maritime pine transcriptome. BMC Genomics 12:366. doi:10.1186/1471-2164-12-366

    Article  PubMed  PubMed Central  Google Scholar 

  • Franceschi VR, Krokene P, Christiansen E, Krekling T (2005) Anatomical and chemical defenses of conifer bark against bark beetles and other pests. The New phytologist 167:353–375. doi:10.1111/j.1469-8137.2005.01436.x

    Article  CAS  PubMed  Google Scholar 

  • Gordon TR, Kirkpatrick SC, Aegerter BJ, Fisher AJ, Storer AJ, Wood DL (2011) Evidence for the occurrence of induced resistance to pitch canker, caused by Gibberella circinata (anamorph Fusarium circinatum), in populations of Pinus radiata. For Pathol 41:227–232. doi:10.1111/j.1439-0329.2010.00678.x

    Google Scholar 

  • Gordon TR, Swett CL, Wingfield MJ (2015) Management of Fusarium diseases affecting conifers. Crop Prot 73:28–39. doi:10.1016/j.cropro.2015.02.018

    Article  Google Scholar 

  • Gotz S et al (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435. doi:10.1093/nar/gkn176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hall DE et al (2013) Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana). BMC Plant Biol 13:80. doi:10.1186/1471-2229-13-80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hodge GR, Dvorak SW (2000) Differential responses of Central American and Mexican pine species and Pinus radiata to infection by the pitch canker fungus. New For 19:241–258

    Article  Google Scholar 

  • Jain M, Srivastava PL, Verma M, Ghangal R, Garg R (2016) De novo transcriptome assembly and comprehensive expression profiling in Crocus sativus to gain insights into apocarotenoid biosynthesis. Scientific reports 6:22456. doi:10.1038/srep22456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jin J, Tian F, Yang D-C, Meng Y-Q, Kong L, Luo J, Gao G (2016) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. doi:10.1093/nar/gkw982

    Google Scholar 

  • Kaliff M, Staal J, Myrenås M, Dixelius C (2007) ABA is required for Leptosphaeria maculans resistance via ABI1- and ABI4-dependent signaling. Mol Plant Microbe In 20:335–345. doi:10.1094/MPMI-20-4-0335

    Article  CAS  Google Scholar 

  • Kayihan GC, Huber DA, Morse AM, White TL, Davis JM (2005) Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine TAG theoretical and applied genetics. Theoretische und angewandte Genetik 110:948–958. doi:10.1007/s00122-004-1915-2

    Article  PubMed  Google Scholar 

  • Kovalchuk A, Kerio S, Oghenekaro AO, Jaber E, Raffaello T, Asiegbu FO (2013) Antimicrobial defenses and resistance in forest trees: challenges and perspectives in a genomic era. Annu Rev Phytopathol 51:221–244. doi:10.1146/annurev-phyto-082712-102307

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. doi:10.1186/gb-2009-10-3-r25

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu D, Raghothama KG, Hasegawa PM, Bressan RA (1994) Osmotin overexpression in potato delays development of disease symptoms. Proc Natl Acad Sci U S A 91:1888–1892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu JJ, Sturrock R, Ekramoddoullah AK (2010) The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function. Plant Cell Rep 29:419–436. doi:10.1007/s00299-010-0826-8

    Article  CAS  PubMed  Google Scholar 

  • Liu JJ, Sturrock RN, Benton R (2013) Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola. BMC Genomics 14:884. doi:10.1186/1471-2164-14-884

    Article  PubMed  PubMed Central  Google Scholar 

  • Mackay J et al (2012) Towards decoding the conifer giga-genome. Plant Mol Biol 80:555–569. doi:10.1007/s11103-012-9961-7

    Article  CAS  PubMed  Google Scholar 

  • Mahomed W, Berg N (2011) EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi. BMC Plant Biol 11:167. doi:10.1186/1471-2229-11-167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mann IK, Wegrzyn JL, Rajora OP (2013) Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource. BMC Genomics 14:702. doi:10.1186/1471-2164-14-702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin-Rodrigues N, Espinel S, Sanchez-Zabala J, Ortiz A, Gonzalez-Murua C, Dunabeitia MK (2013) Spatial and temporal dynamics of the colonization of Pinus radiata by Fusarium circinatum, of conidiophora development in the pith and of traumatic resin duct formation. The New phytologist 198:1215–1227. doi:10.1111/nph.12222

    Article  CAS  PubMed  Google Scholar 

  • Matheson AC, Devey ME, Gordon TR, Werner W, Vogler DR, Balocchi C, Carson MJ (2006) Heritability of response to inoculation by pine pitch canker of seedlings of radiata pine. Australian Forestry Journal 70:101–106

    Article  Google Scholar 

  • Miranda M, Ralph SG, Mellway R, White R, Heath MC, Bohlmann J, Constabel CP (2007) The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins. Molecular plant-microbe interactions : MPMI 20:816–831. doi:10.1094/MPMI-20-7-0816

    Article  CAS  PubMed  Google Scholar 

  • Moraga-Suazo P et al (2014) Development of a genetic linkage map for Pinus radiata and detection of pitch canker disease resistance associated. QTLs Trees 28:1823–1835. doi:10.1007/s00468-014-1090-2

    Article  CAS  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. doi:10.1038/nmeth.1226

    Article  CAS  PubMed  Google Scholar 

  • Muller T, Ensminger I, Schmid KJ (2012) A catalogue of putative unique transcripts from Douglas-fir (Pseudotsuga menziesii) based on 454 transcriptome sequencing of genetically diverse, drought stressed seedlings. BMC Genomics 13:673. doi:10.1186/1471-2164-13-673

    Article  PubMed  PubMed Central  Google Scholar 

  • Myburg H et al (2006) Differential gene expression in loblolly pine (Pinus taeda L.) challenged with the fusiform rust fungus, Cronartium quercuum f.sp. fusiforme. Physiol Mol Plant Pathol 68:79–91. doi:10.1016/j.pmpp.2006.07.002

    Article  CAS  Google Scholar 

  • Neale DB et al (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15:R59. doi:10.1186/gb-2014-15-3-r59

    Article  PubMed  PubMed Central  Google Scholar 

  • Nirenberg I, O'Donnell K (1998) New Fusarium species and combinations within the Gibberella fujikuroi species complex. Mycologia 90:434–458

    Article  Google Scholar 

  • Niu SH, Li ZX, Yuan HW, Chen XY, Li Y, Li W (2013) Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinus phylogeny. BMC Genomics 14:263. doi:10.1186/1471-2164-14-263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 11:180. doi:10.1186/1471-2164-11-180

    Article  PubMed  PubMed Central  Google Scholar 

  • Pascual MB, Cánovas FM, Ávila C (2015) The NAC transcription factor family in maritime pine (Pinus Pinaster): molecular regulation of two genes involved in stress responses. BMC Plant Biology 15:254. doi:10.1186/s12870-015-0640-0

  • Patel RK, Jain M (2012) NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619. doi:10.1371/journal.pone.0030619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quesada T et al (2010) Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.) Genetics 186:677–686. doi:10.1534/genetics.110.117549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rakwal R, Yang G, Komatsu S (2004) Chitinase induced by jasmonic acid, methyl jasmonate, ethylene and protein phosphatase inhibitors in rice. Mol Biol Rep 31:113–119

    Article  CAS  PubMed  Google Scholar 

  • Rigault P, Boyle B, Lepage P, Cooke JE, Bousquet J, MacKay JJ (2011) A white spruce gene catalog for conifer genome analyses. Plant Physiol 157:14–28. doi:10.1104/pp.111.179663

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robert-Seilaniantz A, Grant M, Jones JD (2011) Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. Annu Rev Phytopathol 49:317–343. doi:10.1146/annurev-phyto-073009-114447

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez A, Shimada T, Cervera M, Alquézar B, Gaeda J, Gómez-Cárdenas A, De Ollas CJ, Rodrigo MJ, Zacarías L, Peña L (2014) Terpene down-regulation triggers defense responses in transgenic orange leading to resistance against fungal pathogens. Plant Physiol 164(1):321–339

  • Rogers DL (2002) In situ genetic conservation of Monterey pine (Pinus radiata D. Don): Information and recommendations Report No 26 University of California Division of Agriculture and Natural Resources Genetic Resources Conservation Program, Davis CA USA.

  • Rogers DL (2004) In situ genetic conservation of a naturally restricted and commercially widespread species. Pinus radiata Forest Ecology and Management 197:311–322. doi:10.1016/j.foreco.2004.05.022

  • Roux J, Eisenberg B, Kanzler A, Nel A, Coetzee V, Kietzka E, Wingfield MJ (2006) Testing of selected South African Pinus hybrids and families for tolerance to the pitch canker pathogen. Fusarium circinatum New Forests 33:109–123. doi:10.1007/s11056-006-9017-4

    Article  Google Scholar 

  • Schlink K (2009) Identification and characterization of differentially expressed genes from Fagus sylvatica roots after infection with Phytophthora citricola. Plant Cell Rep 28:873–882. doi:10.1007/s00299-009-0694-2

    Article  CAS  PubMed  Google Scholar 

  • Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species American journal of botany 99:257–266 doi:10.3732/ajb.1100292

  • Sun H, Paulin L, Alatalo E, Asiegbu FO (2011) Response of living tissues of Pinus sylvestris to the saprotrophic biocontrol fungus Phlebiopsis gigantea. Tree Physiol 31:438–451. doi:10.1093/treephys/tpr027

    Article  PubMed  Google Scholar 

  • Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21:2213–2223. doi:10.1101/gr.124321.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thimm O et al (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant journal: for cell and molecular biology 37:914–939

    Article  CAS  Google Scholar 

  • Thoungchaleun V, Kim KW, Lee DK, Chang CS, Park EW (2008) Pre-infection behavior of the pitch canker fungus fusarium circinatum on pine stems. The Plant Pathology Journal 24(2):112–117

    Article  Google Scholar 

  • Ton J, Mauch-Mani B (2004) β-amino-butyric acid-induced resistance against necrotrophic pathogens is based on ABA-dependent priming for callose. Plant J 38:119–130. doi:10.1111/j.1365-313X.2004.02028.x

    Article  CAS  PubMed  Google Scholar 

  • Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, et al. (2007) Legume transcription factors: global regulators of plant development and response to the environment. Plant Physiol 144:538–549

  • Usadel B et al (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138:1195–1204. doi:10.1104/pp.105.060459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Veluthakkal R, Dasgupta M (2010) Pathogenesis-related genes and proteins in forest tree species. Trees 24:993–1006. doi:10.1007/s00468-010-0489-7

    Article  CAS  Google Scholar 

  • Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S (2015) Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics 16:1057. doi:10.1186/s12864-015-2277-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63. doi:10.1038/nrg2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Li P, Brutnell TP (2010) Exploring plant transcriptomes using ultra high-throughput sequencing. Briefings in functional genomics 9:118–128. doi:10.1093/bfgp/elp057

    Article  CAS  PubMed  Google Scholar 

  • Wegrzyn JL et al (2013) Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. PLoS One 8:e72439. doi:10.1371/journal.pone.0072439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wegrzyn JL et al (2014) Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics 196:891–909. doi:10.1534/genetics.113.159996

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wingfield MJ, Hammerbacher A, Ganley RJ, Steenkamp ET, Gordon TR, Wingfield BD, Coutinho TA (2008) Pitch canker caused by Fusarium circinatum—a growing threat to pine plantations and forests worldwide. Australas Plant Pathol 37:319–334

    Article  Google Scholar 

  • Zhang Y, Zhang S, Han S, Li X, Qi L (2012) Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). Plant Cell Rep 31:1637–1657. doi:10.1007/s00299-012-1277-1

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Facultad de Ciencias Forestales, Universidad de Concepción, Victoria 631, Concepción, Chile

    Angela Carrasco, Ricardo Durán, Marta Fernández & Sofía Valenzuela

  2. Department of Plant Sciences, University of California Davis, Davis, CA, USA

    Jill L. Wegrzyn & David Neale

  3. Centro de Biotecnología, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile

    Marta Fernández, Andrea Donoso, Victoria Rodriguez & Sofía Valenzuela

Authors
  1. Angela Carrasco
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jill L. Wegrzyn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ricardo Durán
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marta Fernández
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Andrea Donoso
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Victoria Rodriguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. David Neale
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sofía Valenzuela
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sofía Valenzuela.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Communicated by S. C. González-Martínez

Electronic supplementary material

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)

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)

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)

Online resource Table 1

(XLSX 11 kb)

Online resource Table 2

(XLSX 14 kb)

Online resource Table 3

(XLSX 12 kb)

Online resource Table 4

(XLSX 620 kb)

Online resource Table 5

(XLSX 40 kb)

Online resource Table 6

(XLSX 57 kb)

Online resource Table 7

(XLSX 150 kb)

Data archiving statement

The raw data reported in this investigation are archived and publicly available at the National Center for Biotechnology Information in the Bioproject repository, under the accession number PRJNA295331 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA295331).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Carrasco, A., Wegrzyn, J.L., Durán, R. et al. Expression profiling in Pinus radiata infected with Fusarium circinatum . Tree Genetics & Genomes 13, 46 (2017). https://doi.org/10.1007/s11295-017-1125-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-017-1125-0

Keywords

Search

Navigation