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| Status |
Public on Jan 30, 2022 |
| Title |
Cicer arietinum roots inoculated with Phytophthora medicaginis_72hpi_rep1 |
| Sample type |
SRA |
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| Source name |
Cicer arietinum roots inoculated with Phytophthora medicaginis mycellium
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| Organisms |
Cicer arietinum; Phytophthora medicaginis |
| Characteristics |
tissue: Root and mycellium
treatment: 72 hours post inoculation
diseased state: diseased
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| Treatment protocol |
Roots were inoculated with P. medicaginis mycellial agar blocks 1 cm from the root tip and harvested at 12, 24 and 72 hpi. P. medicaginis axenically growing on V8 juice media were transferred to full strength MS media for 12 hours before harvesting mycellium.
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| Growth protocol |
Chickpea var. 'Sonali' seeds were surface sterilised (4% NaOCl solution for 15 min, 70% EtOH for ten minutes and sterile ddH2O rinse three times) before sowing on modified full strength Murashige and Skoog agar plates (4.4% MS; 3% CaCO3, pH 7, 1.1% bacto agar) supplemented with Gamborg’s vitamins. Seedlings were grown in controlled growth chambers with 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 500 μmol m-2 s-1 light intensity. Fifteen-day old seedlings were used for inoculation. P. medicaginis isolate TR7831 was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. Prior to inoculations, P. medicaginis was passaged through the host to ensure pathogenicity, and after reisolating on V8 juice agar plates supplemented with ampicillin (100 ug mL-1), the 2rd generation of P. medicaginis was used to prepare inoculum. P. medicaginis inoculum (3rd generation) was prepared one day before inoculations by aseptically transferring mycelial agar blocks taken from the edge of an actively growing culture onto 0.5 x 0.5 mm2 sterile membranes overlaid on V8 juice agar plates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Root samples flash frozen with liquen nitrogen; RNA was extracted using the Bioline Plant II RNA extraction kit according to the manufacturer’s guidelines.
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Cicer arietinum variety 'Sonali' and Phytophthora medicaginis isolate 7831
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| Data processing |
Raw RNA-sequencing reads were trimmed with default parameters, and then aligned to the primary transcripts of the Cicer arietinum Desi genome (Jain et al., 2013) using CLC Genomics Workbench 10. For the alignment, the minimum length fraction was set to 0.9, the minimum similarity fraction 0.9 and the maximum number of hits per read was 10 while all other parameters were set to default.
Total gene reads were calculated using CLC Genomics Workbench 10.
Genome_build: Cicer arietinum Desi genome primary transcripts (Jain, M., Misra, G., Patel, R. K., Priya, P., Jhanwar, S., Khan, A. W., Shah, N., Singh, V. K., Garg, R., Jeena, G., Yadav, M., Kant, C., Sharma, P., Yadav, G., Bhatia, S., Tyagi, A. K. & Chattopadhyay, D. 2013. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). The Plant Journal, 74, 715-729.)
Supplementary_files_format_and_content: Matrix table of the raw gene counts for every Cicer arietinum gene and every sample
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| Submission date |
Aug 25, 2021 |
| Last update date |
Jan 30, 2022 |
| 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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| Platform ID |
GPL30539 |
| Series (1) |
| GSE182741 |
Chickpea Roots Undergoing Colonisation by Phytophthora medicaginis do not Display Hormone Accumulation nor Signalling Typically Associated with Model Leaf Hemibiotrophic Diseases |
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| Relations |
| BioSample |
SAMN20970470 |
| SRA |
SRX11905161 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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