Whole genome wide expression profiles of Vitis amurensisgrape responding to downy mildew by using Solexa sequencing technology

Abstract

BackgroundDowny mildew (DM), caused by pathogen Plasmopara viticola (PV) is the single most damaging disease of grapes (Vitis L.) worldwide. However, the mechanisms of the disease development in grapes are poorly understood. A method for estimating gene expression levels using Solexa sequencing of Type I restriction-endonuclease-generated cDNA fragments was used for deep sequencing the transcriptomes resulting from PV infected leaves of Vitis amurensis Rupr. cv. Zuoshan-1. Our goal is to identify genes that are involved in resistance to grape DM disease.ResultsApproximately 8.5 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from PV pathogen-infected leaves, and about 7.5 M were sequenced from the cDNA library constructed from the control leaves. When annotated, a total of 15,249 putative genes were identified from the Solexa sequencing tags for the infection (INF) library and 14,549 for the control (CON) library. Comparative analysis between these two cDNA libraries showed about 0.9% of the unique tags increased by at least five-fold, and about 0.6% of the unique tags decreased more than five-fold in infected leaves, while 98.5% of the unique tags showed less than five-fold difference between the two samples. The expression levels of 12 differentially expressed genes were confirmed by Real-time RT-PCR and the trends observed agreed well with the Solexa expression profiles, although the degree of change was lower in amplitude. After pathway enrichment analysis, a set of significantly enriched pathways were identified for the differentially expressed genes (DEGs), which associated with ribosome structure, photosynthesis, amino acid and sugar metabolism.ConclusionsThis study presented a series of candidate genes and pathways that may contribute to DM resistance in grapes, and illustrated that the Solexa-based tag-sequencing approach was a powerful tool for gene expression comparison between control and treated samples.

Cultivar-specific kinetics of gene induction during downy mildew early infection in grapevine

“…Hpi hours post infection; FC fold change, white bars: microarray computed fold change of the average expression levels under two conditions (RankProd), dark bars: qPCR based fold change calculated as 2^Δ ΔCT al. 2010; Wu et al 2010), also for this interaction, it has recently been reported an up-regulation of photosynthesisrelated transcripts in a resistant grapevine genotype at 12 hpi (Malacarne et al 2011).…”

“…Advances toward the elucidation of this specific pathosystem have been made using several approaches from transcriptional analysis (Figueiredo et al 2008;Kortekamp et al 2008;Polesani et al 2008;Polesani et al 2010;Wu et al 2010;Malacarne et al 2011) to quantitative trait loci (QTL) analysis of segregating populations (Dalbo et al 2000;Wiedemann-Merdinoglu et al 2003;Fischer et al 2004;Welter et al 2007;Bellin et al 2009;Peressoti et al 2010;Blasi et al 2011;Schwander et al 2011). Despite all the knowledge gathered on grapevinedowny mildew interaction, recent reports documented the emergence of P. viticola resistance-breaking isolates in Europe (Peressotti et al 2010).…”

The Streptococcus suis transcriptional landscape reveals adaptation mechanisms in pig blood and cerebrospinal fluid

“…In the present work, the differentially expressed genes between each of the two samples were screened with the threshold of FDR < 0.001 and the absolute value of log 2 ratio ≥ 1 (Wu et al 2010a). …”

Isolation of a WRKY30 gene from Muscadinia rotundifolia (Michx) and validation of its function under biotic and abiotic stresses

“…Inoculation of P. viticola was referred to Wu et al (2010). Briefly, the fourth unfolded leaves from the shoot apex were harvested from each of three vines, and the three leaves were combined to represent one replicate.…”