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| Status |
Public on Aug 05, 2024 |
| Title |
Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis |
| Organisms |
Cicer arietinum; Phytophthora medicaginis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Introduction: Hemibiotrophic Phytophthora are a group of agriculturally and ecologically important pathogenic oomycetes causing severe decline in plant growth and fitness. The lifestyle of these pathogens consists of an initial biotrophic phase followed by a switch to a necrotrophic phase in the latter stages of infection. Between these two phases is the biotrophic to necrotrophic switch (BNS) phase, the timing and controls of which are not well understood particularly in Phytophthora spp. where host resistance has a purely quantitative genetic basis.
Methods: To investigate this we sequenced and annotated the genome of Phytophthora medicaginis, causal agent of root rot and substantial yield losses to Fabaceae hosts. We analysed the transcriptome of P. medicaginis across three phases of colonisation of a susceptible chickpea host (Cicer arietinum) and performed co-regulatory analysis to identify putative small secreted protein (SSP) effectors that influence timing of the BNS in a quantitative pathosystem.
Results: The genome of P. medicaginis is ~78 Mb, comparable to P. fragariae and P. rubi which also cause root rot. Despite this, it encodes the second smallest number of RxLR (arginine-any amino acid-leucine-arginine) containing proteins of currently sequenced Phytophthora species. Only quantitative resistance is known in chickpea to P. medicaginis, however, we found that many RxLR, Crinkler (CRN), and Nep1-like protein (NLP) proteins and carbohydrate active enzymes (CAZymes) were regulated during infection. Characterisation of one of these, Phytmed_10271, which encodes an RxLR effector demonstrates that it plays a role in the timing of the BNS phase and root cell death.
Discussion: These findings provide an important framework and resource for understanding the role of pathogenicity factors in purely quantitative Phytophthora pathosystems and their implications to the timing of the BNS phase.
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| Overall design |
In total six samples were generated for the double stranded interfering RNA knockdown experiment to test the function of Phytmed_10271 in Phytophthora medicaginis during their biotrophic to necrotrophic switch in chickpea roots. Three of the samples were from dsiRNA treated roots targeting Phytmed_10271 and the other three samples were from roots treated with scrambled dsiRNA unable to target any endogenous P. medicaginis genes. Additionally, 16 samples were generated for RNA-sequencing of which the 16 samples included 1 replicate each of 16 timepoints 8, 16, 20, 28, 32, 36, 40, 44, 48, 60, 84, 96, 108, 120, 132 and 144 hours post P. medicaginis inoculation in chickpea var. 'Sonali' roots.
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| Contributor(s) |
Coles DW, Bithell SL, Jeffries T, Cuddy WS, Plett JM |
| Citation(s) |
39224851 |
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| Submission date |
Sep 07, 2021 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Jonathan Michael Plett |
| E-mail(s) |
J.Plett@westernsydney.edu.au
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| Phone |
+61 422535833
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| Organization name |
Western Sydney University
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| Department |
Soil Biology and Genomics
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| Lab |
Plett laboratory
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| Street address |
50 Bourke street
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| City |
Sydney |
| State/province |
New South Wales |
| ZIP/Postal code |
2753 |
| Country |
Australia |
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| Platforms (2) |
| GPL30598 |
Illumina HiSeq 4000 (Cicer arietinum; Phytophthora medicaginis) |
| GPL33212 |
Illumina HiSeq 2500 (Cicer arietinum; Phytophthora medicaginis) |
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| Samples (22)
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| GSM5563294 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_8hpi_rep1 |
| GSM5563295 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_16hpi_rep1 |
| GSM5563296 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_20hpi_rep1 |
| GSM5563297 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_28hpi_rep1 |
| GSM5563298 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_32hpi_rep1 |
| GSM5563299 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_36hpi_rep1 |
| GSM5563300 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_40hpi_rep1 |
| GSM5563301 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_44hpi_rep1 |
| GSM5563302 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_48hpi_rep1 |
| GSM5563303 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_60hpi_rep1 |
| GSM5563304 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_84hpi_rep1 |
| GSM5563305 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_96hpi_rep1 |
| GSM5563306 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_108hpi_rep1 |
| GSM5563307 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_120hpi_rep1 |
| GSM5563308 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_132hpi_rep1 |
| GSM5563309 |
Cicer arietinum roots inoculated with Phytophthora medicaginis_144hpi_rep1 |
| GSM7081483 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_A, 24hpi |
| GSM7081484 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_B, 24hpi |
| GSM7081485 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, phytmed 10271_kd_C, 24hpi |
| GSM7081486 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_A, 24hpi |
| GSM7081487 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_B, 24hpi |
| GSM7081488 |
Cicer arietinum lateral roots inoculated with Phytophthora medicaginis, scrambled_C, 24hpi |
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| Relations |
| BioProject |
PRJNA761393 |
| SRA |
SRP336033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183604_Processed_data_1.txt.gz |
405.9 Kb |
(ftp)(http) |
TXT |
| GSE183604_Processed_data_2.txt.gz |
891.6 Kb |
(ftp)(http) |
TXT |
| GSE183604_processed_data_Cicerari.txt.gz |
588.6 Kb |
(ftp)(http) |
TXT |
| GSE183604_processed_data_Phytmed.txt.gz |
266.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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