Fig 1.
Infection of lupin roots by P. parasitica.
(A) Percentage of roots with visible lesions during the infection time course, 0 hpi to 60 hpi. (n = 12). (B) Transverse hand section of a lupin root inoculated with P. parasitica zoospores. By 27 hpi, P. parasitica hyphae grow both intercellularly (arrowheads) and intracellularly (arrows) during colonisation of the root cortex. Scale bar = 50 μm. (C) Ratio of P. parasitica DNA:lupin DNA as determined by qPCR measurement of the levels of the P. parasitica WS041 gene and the lupin nitrilase gene 4A (NIT4A). Data are from the three biological replicates chosen for RNA-Seq transcriptome analysis. P. parasitica DNA was not detected in mock-inoculated or 12 hpi or 18 hpi samples. Error bars indicate the standard error of the mean.
Table 1.
CWDEs in the top 200 differentially expressed genes between 30 hpi and 60 hpi.
Fig 2.
Total NRPKs from the multiple location data set for genes targeting major categories of wall components.
Because many genes act on cellulose and hemicelluloses, counts for these two substrates have been combined. (A) Total NRPK counts show the relative transcript abundance for each substrate category. (B) Total NRPK counts expressed as a percentage of the maximum counts show trends in the expression profiles over time. Genes whose products target pectins have been assigned to the first and second halves of the 60-h infection time-course.
Fig 3.
Summary of expression profiles of P. parasitica CWDEs during the infection of lupin roots.
The top row shows representations of the six main expression profiles displayed by P. parasitica CWDEs. CAZyme families have been assigned to putative polysaccharide category according to homology with characterised CAZymes. Within each major wall polysaccharide category, the NRPK values of CAZyme family members whose expression peaks at the same time (the number of genes is shown in the column labelled #) have been summed and the total peak NRPK value shown in the columns labelled NRPK. CAZyme families whose members act on multiple substrates are indicated by superscripts. These CAZyme families have be allocated to a selected substrate according to recent literature on their most likely function. The superscripts indicate their possible targets: ipectin and glycoproteins; iipectin, hemicellulose and glycoproteins; iiicellulose and β-1,3-glucans; ivcellulose, hemicellulose and glycoproteins; vhemicellulose and glycoproteins; vihemicellulose and β-1,3-glucans.
Fig 4.
Representation of the percentage of NRPK counts for each CWDE family during early (green, 30–36 hpi), middle (yellow, 42–48 hpi) and late (red, 54–60 hpi) infection of lupin roots as a percentage of the total number of NRPK counts from all CWDEs predicted to target a particular substrate.
The total number of NRPK counts for each substrate are shown below the columns. The inset at the top shows the relative heights (transcript abundance) for the different substrate categories. HG: homogalacturonan; RGI: rhamnogalacturonan I.