SuperSAGE revealed different classes of early resistance response genes in Capsicum chinense plants harboring L 3 -resistance gene infected with Pepper mild mottle virus

  • Hiroyuki Hamada
  • Hideo Matsumura
  • Reiko Tomita
  • Ryohei Terauchi
  • Kazumi Suzuki
  • Kappei KobayashiEmail author
Viral and Viroid Diseases


We used SuperSAGE, an improved version of serial analysis of gene expression, to explore transcriptome changes early in the L 3 -mediated resistance response of pepper plants against a tobamovirus. Capsicum chinense plants homozygous for the L 3 resistance gene were infected with virulent and avirulent strains of Pepper mild mottle virus (PMMoV). Plants were maintained at a temperature nonpermissive for the resistance gene to allow the viruses to spread, then transferred to a permissive temperature for 3 h and subsequently analyzed. In the incompatible reaction, we selected 152 SuperSAGE tags (each 26 nucleotides long) possibly corresponding to upregulated genes, and 84 tags for downregulated genes. Approximately 70% of tags had matching ESTs in the genus Capsicum, other genera within the Solanaceae and/or other families of plants. More than 90% of tags with EST matches could be annotated with either functionally characterized or uncharacterized proteins. We compared genes annotated by SuperSAGE tags and those annotated by partial cDNA that was obtained using the SuperSAGE tag sequences as rapid amplification of the cDNA ends-PCR primers. Of genes annotated by SuperSAGE tags, c. 90% were consistent with those annotated by longer cDNA sequences. We cloned 17 full-length cDNAs from different SuperSAGE tags and confirmed that these genes were upregulated during normal infection in the incompatible interaction. We identified several early resistance response genes including a Ran/TC4 protein and a β-oxidation multifunctional protein, indicating that SuperSAGE is a powerful tool for investigating plant–pathogen interactions.


Early response L3 PMMoV Resistance SuperSAGE Transcriptome 



We thank Dr. K. W. Kinzler for SAGE2000 software, Harumi Takahashi and Kazue Obara for technical assistance and all members of IBRC for fruitful discussion. This study was supported in part by the Iwate Prefecture Government and in part by a grant-in-aid for Scientific Research (C) (18580047) from the Japan Society for the Promotion of Science.

Supplementary material

10327_2008_106_MOESM1_ESM.doc (48 kb)
Tables S1 and S2 (DOC 47 kb)
10327_2008_106_MOESM2_ESM.tif (1.4 mb)
Fig. S1. Real-time PCR analysis for mRNA levels of SuperSAGE-tagged genes in normal infection process at 96 h postinoculation. C. chinense plants harboring the L 3 resistance gene were inoculated with P1,2 (filled column) or P1,2,3 (gray column) pathotypes of PMMoV or phosphate buffer (mock inoculation; open column). Total RNA was extracted from inoculated leaves at 96 h postinoculation for real-time PCR using primers in Table S1 and normalized against 18S rRNA levels. The mRNA levels relative to untreated plants were determined in two independent RNA preparations, and mean values are shown. (TIFF 240 kb)


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Copyright information

© The Phytopathological Society of Japan and Springer 2008

Authors and Affiliations

  • Hiroyuki Hamada
    • 1
    • 2
  • Hideo Matsumura
    • 1
  • Reiko Tomita
    • 1
  • Ryohei Terauchi
    • 1
  • Kazumi Suzuki
    • 1
    • 3
  • Kappei Kobayashi
    • 1
    Email author
  1. 1.Iwate Biotechnology Research CenterKitakamiJapan
  2. 2.National Agricultural Research CenterNational Agriculture and Food Research OrganizationTsukubaJapan
  3. 3.School of Environmental ScienceUniversity of Shiga PrefectureHikoneJapan

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