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The effect on the transcriptome of Anemone coronaria following infection with rust (Tranzschelia discolor).

Laura M, Borghi C, Bobbio V, Allavena A - PLoS ONE (2015)

Bottom Line: Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank.Only one R gene (PGIP) was up-regulated.The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

View Article: PubMed Central - PubMed

Affiliation: CRA-Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy.

ABSTRACT
In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3'end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

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Gene expression in Anemone coronaria infected with Tranzschelia discolor.Expression analysis was conducted among sample A (plants analyzed by pyrosequencing) and samples B and C, each composed of five distinct uninfected and infected plants. Ten plant DTAs genes (five up- and five down-regulated) putatively involved in the response to Tranzschelia discolor infection and three fungal genes, were tested. The data were normalized using Anemone coronaria 18s rRNA gene as the reference. Expression analysis was performed in triplicate on three biological replicates. Transcript abundance data were expressed in the form mean ± standard error (SE).
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pone.0118565.g008: Gene expression in Anemone coronaria infected with Tranzschelia discolor.Expression analysis was conducted among sample A (plants analyzed by pyrosequencing) and samples B and C, each composed of five distinct uninfected and infected plants. Ten plant DTAs genes (five up- and five down-regulated) putatively involved in the response to Tranzschelia discolor infection and three fungal genes, were tested. The data were normalized using Anemone coronaria 18s rRNA gene as the reference. Expression analysis was performed in triplicate on three biological replicates. Transcript abundance data were expressed in the form mean ± standard error (SE).

Mentions: The qPCR analysis based on ten plant and three fungal target results (unigenes) confirmed that the 3’ sequencing of non-normalized libraries was informative with respect to recognizing DTAs. qPCR data of sample A (plants analyzed by pyrosequencing) were compared with qPCR data of samples B and C, each composed of five distinct uninfected and infected plants. Significant differences in expression was observed for the 13 genes tested (Fig. 8 and Table 1). The up regulated genes showed the same behavior, whereas down regulated genes varied significantly likely as a result of sample bias at low expression levels. In addition, divergences in level of gene expression may reflect time points of the plant/pathogen interaction or the genetic eterogenicity in A. coronaria population.


The effect on the transcriptome of Anemone coronaria following infection with rust (Tranzschelia discolor).

Laura M, Borghi C, Bobbio V, Allavena A - PLoS ONE (2015)

Gene expression in Anemone coronaria infected with Tranzschelia discolor.Expression analysis was conducted among sample A (plants analyzed by pyrosequencing) and samples B and C, each composed of five distinct uninfected and infected plants. Ten plant DTAs genes (five up- and five down-regulated) putatively involved in the response to Tranzschelia discolor infection and three fungal genes, were tested. The data were normalized using Anemone coronaria 18s rRNA gene as the reference. Expression analysis was performed in triplicate on three biological replicates. Transcript abundance data were expressed in the form mean ± standard error (SE).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359109&req=5

pone.0118565.g008: Gene expression in Anemone coronaria infected with Tranzschelia discolor.Expression analysis was conducted among sample A (plants analyzed by pyrosequencing) and samples B and C, each composed of five distinct uninfected and infected plants. Ten plant DTAs genes (five up- and five down-regulated) putatively involved in the response to Tranzschelia discolor infection and three fungal genes, were tested. The data were normalized using Anemone coronaria 18s rRNA gene as the reference. Expression analysis was performed in triplicate on three biological replicates. Transcript abundance data were expressed in the form mean ± standard error (SE).
Mentions: The qPCR analysis based on ten plant and three fungal target results (unigenes) confirmed that the 3’ sequencing of non-normalized libraries was informative with respect to recognizing DTAs. qPCR data of sample A (plants analyzed by pyrosequencing) were compared with qPCR data of samples B and C, each composed of five distinct uninfected and infected plants. Significant differences in expression was observed for the 13 genes tested (Fig. 8 and Table 1). The up regulated genes showed the same behavior, whereas down regulated genes varied significantly likely as a result of sample bias at low expression levels. In addition, divergences in level of gene expression may reflect time points of the plant/pathogen interaction or the genetic eterogenicity in A. coronaria population.

Bottom Line: Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank.Only one R gene (PGIP) was up-regulated.The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

View Article: PubMed Central - PubMed

Affiliation: CRA-Unità di Ricerca per la Floricoltura e le Specie Ornamentali, Corso Inglesi 508, 18038 Sanremo (IM), Italy.

ABSTRACT
In order to understand plant/pathogen interaction, the transcriptome of uninfected (1S) and infected (2I) plant was sequenced at 3'end by the GS FLX 454 platform. De novo assembly of high-quality reads generated 27,231 contigs leaving 37,191 singletons in the 1S and 38,393 in the 2I libraries. ESTcalc tool suggested that 71% of the transcriptome had been captured, with 99% of the genes present being represented by at least one read. Unigene annotation showed that 50.5% of the predicted translation products shared significant homology with protein sequences in GenBank. In all 253 differential transcript abundance (DTAs) were in higher abundance and 52 in lower abundance in the 2I library. 128 higher abundance DTA genes were of fungal origin and 49 were clearly plant sequences. A tBLASTn-based search of the sequences using as query the full length predicted polypeptide product of 50 R genes identified 16 R gene products. Only one R gene (PGIP) was up-regulated. The response of the plant to fungal invasion included the up-regulation of several pathogenesis related protein (PR) genes involved in JA signaling and other genes associated with defense response and down regulation of cell wall associated genes, non-race-specific disease resistance1 (NDR1) and other genes like myb, presqualene diphosphate phosphatase (PSDPase), a UDP-glycosyltransferase 74E2-like (UGT). The DTA genes identified here should provide a basis for understanding the A. coronaria/T. discolor interaction and leads for biotechnology-based disease resistance breeding.

Show MeSH
Related in: MedlinePlus