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Transcriptome characterization and expression profiling in chestnut cultivars resistant or susceptible to the gall wasp Dryocosmus kuriphilus

  • Alberto Acquadro
  • Daniela Torello MarinoniEmail author
  • Chiara Sartor
  • Francesca Dini
  • Matteo Macchio
  • Roberto Botta
Original Article

Abstract

The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid ‘Bouche de Bétizac’ (BB) and the susceptible cultivar ‘Madonna’ (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as “response to stimulus” (GO:0050896), and “developmental processes” (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in “post-embryonic development”. Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives.

Keywords

RNA-seq Castanea Resistance Assembly Gene ontology 

Notes

Acknowledgements

Research founded by Regione Piemonte Administration and by the cooperation program Italy-France Alcotra Project: Salvaguardia dell’ecosistema castagno.

Compliance with ethical standards

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

Conflict of interest

The authors declare that they have no conflict of interest and in particular: Alberto Acquadro declare that he has no conflict of interest. Daniela Torello Marinoni declare that she has no conflict of interest. Chiara Sartor declare that she has no conflict of interest. Francesca Dini declare that she has no conflict of interest. Matteo Macchio declare that he has no conflict of interest. Roberto Botta declare that he has no conflict of interest.

Supplementary material

438_2019_1607_MOESM1_ESM.fa (41.7 mb)
Supplementary material 1 (FA 42664 kb). The assembled transcriptome of the cultivar ‘Bouche de Bétizac’, filtered for contaminants deriving from pests and fungi
438_2019_1607_MOESM2_ESM.fa (30.7 mb)
Supplementary material 2 (FA 31448 kb). The assembled transcriptome of the cultivar ‘Madonna’
438_2019_1607_MOESM3_ESM.docx (20 kb)
Supplementary material 3 (DOCX 20 kb). CEGMA pipeline results on the C. sativa transcriptome. Prots = Number of 248 ultra-conserved CEGs present in genome; %Completeness = Percentage of 248 ultra-conserved CEGs present; Total = Total number of CEGs present including putative orthologs; Average = Average number of orthologs per CEG; %Ortho = Percentage of detected CEGS that have more than one ortholog
438_2019_1607_MOESM4_ESM.fa (605 kb)
Supplementary material 4 (FA 605 kb). Unigenes, showing homology to 82 univoque proteins out of the 112 encoded reference RGAs, identified
438_2019_1607_MOESM5_ESM.txt (147 kb)
Supplementary material 5 (TXT 146 kb). miRNA targets in cultivar ‘Bouche de Bétizac’
438_2019_1607_MOESM6_ESM.txt (153 kb)
Supplementary material 6 (TXT 153 kb). miRNA targets in cultivar ‘Madonna’
438_2019_1607_MOESM7_ESM.zip (3 kb)
Supplementary material 7 (ZIP 8 kb). Complete statistics for the identified SSR loci
438_2019_1607_MOESM8_ESM.txt (1.9 mb)
Supplementary material 8 (TXT 1954 kb). Primers designed for the selected SSR loci
438_2019_1607_MOESM9_ESM.xlsx (3.6 mb)
Supplementary material 9 (XLSX 3677 kb). List of genes regulated in infested ‘Bouche de Bétizac’ and ‘Madonna transcriptomes
438_2019_1607_MOESM10_ESM.docx (35 kb)
Supplementary material 10 (DOCX 35 kb). List of the genes commonly regulated in “BI vs BNI” and “BI vs MI” (Venn intersection, Fig. 2c) and not regulated in “BNI vs MNI” and “MI vs MNI”
438_2019_1607_MOESM11_ESM.docx (21 kb)
Supplementary material 11 (DOCX 21 kb). Genes showing enriched GO terms among the putative miRNA target transcripts
438_2019_1607_MOESM12_ESM.docx (20 kb)
Supplementary material 12 (DOCX 19 kb). The over-representation of GO terms among the putative miRNA target transcripts. P value (< 0.01) was used to assess statistical significance. AgriGO was used to obtain GO terms from presumptive miRNA target and ReviGO was used to evaluate enriched GO terms
438_2019_1607_MOESM13_ESM.tif (549 kb)
Supplementary material 13 (TIFF 549 kb). Annotation and categorization analysis of the chestnut transcriptome. a Blast2GO results. b Species more represented in the blast analysis and top blast hits. c Chart giving the distribution of the number of annotations (GO terms) retrieved from the different source databases (e.g., UniProt, PDB, TAIR)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.DISAFA, Dipartimento di Scienze Agrarie, Forestali e AlimentariUniversità degli Studi di TorinoGrugliascoItaly

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