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Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots

Ji, H.; Kyndt, T.; Denil, S.; Lindsey, K.; Topping, J.; Nahar, K.; Haegeman, A.; Van Criekinge, W.; Trooskens, G.; De Meyer, T.; Gheysen, G.

Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots Thumbnail


H. Ji

T. Kyndt

S. Denil

K. Nahar

A. Haegeman

W. Van Criekinge

G. Trooskens

T. De Meyer

G. Gheysen


One of the reasons for the progressive yield decline observed in aerobic rice production is the rapid build-up of populations of the rice root knot nematode Meloidogyne graminicola. These nematodes induce specialized feeding cells inside root tissue, called giant cells. By injecting effectors in and sipping metabolites out of these cells, they reprogramme normal cell development and deprive the plant of its nutrients. In this research we have studied the transcriptome of giant cells in rice, after isolation of these cells by laser-capture microdissection. The expression profiles revealed a general induction of primary metabolism inside the giant cells. Although the roots were shielded from light induction, we detected a remarkable induction of genes involved in chloroplast biogenesis and tetrapyrrole synthesis. The presence of chloroplast-like structures inside these dark-grown cells was confirmed by confocal microscopy. On the other hand, genes involved in secondary metabolism and more specifically, the majority of defence-related genes were strongly suppressed in the giant cells. In addition, significant induction of transcripts involved in epigenetic processes was detected inside these cells 7 days after infection.

Journal Article Type Article
Publication Date Sep 1, 2013
Deposit Date Jun 21, 2013
Publicly Available Date May 29, 2014
Journal Journal of Experimental Botany
Print ISSN 0022-0957
Electronic ISSN 1460-2431
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 64
Issue 13
Pages 3885-3898
Keywords Giant cell, Laser-capture microdissection, Meloidogyne graminicola, Oryza sativa, Root knot nematode, Transcriptome.
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Published Journal Article (5.8 Mb)

Copyright Statement
© The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

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