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| Status |
Public on Dec 12, 2023 |
| Title |
SI_4h3 |
| Sample type |
SRA |
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| Source name |
Fludioxonil treat
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| Organism |
Botrytis cinerea |
| Characteristics |
strain: BC-57
tissue: mycelia
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| Treatment protocol |
S (fludioxonil-sensitive), FR (fludioxonil resistance from field), and LR (fludioxonil resistance from laboratory) were routinely cultivated on PDA for three days. For each fungal strain, eight mycelium plugs (5 mm) were incubated using a 200 mL potato dextrose broth (PDB) medium for two days at 23°C and shaken at 180 rpm. The resulting mycelia were treated with or without fludioxonil. In detail, the 10 mg/L fludioxonil stock solutions were added to the PDB medium at final concentrations of 0.05 μg/mL for S, 10 μg/mL for FR, and 500 μg/mL for LR, and the same volume of acetone was added to the 200 mL PDB medium to prepare the control samples. The fludioxonil-induced and no-induced (control) samples were cultured under the same conditions (at 23°C and 180 rpm) for 4 h before RNA extraction. Six samples in total were collected for the following RNA manipulations, i.e., fludioxonil-induced and no-induced S (designated as SI_4h and S_4h), fludioxonil-induced and no-induced LR (designated as LRI_4h and LR_4h), and fludioxonil-induced and no-induced FR (designated as FRI_4h and FR_4h, respec-tively).
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| Growth protocol |
The B. cinerea strains, BC-2 and BC-57, used in this study, were isolated from typical gray mold symptom tomato leaves found in local greenhouses (Beijing City). Both of the B. cinerea isolates were first purified using single spore isolation and thereafter main-tained on potato dextrose agar (PDA, 200 g/L potato, 20 g/L agar, and 20 g/L dextrose). After approximately three days of dark-incubation at 23°C, B. cinerea mycelia were ob-tained from the edge of the colonies and transferred to the PDA slants and preserved at 15°C in darkness.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelium of the parent fludioxonil-sensitive strain (S), laboratory fludioxo-nil-resistant strain (LR), and field fludioxonil-resistant strains were obtained as de-scribed above. All of the isolates were grown at the same time for the same amount of time (three days) under the same conditions (shaking at 23°C and 180 rpm) in PDB. The mycelium were then collected at the same time. RNA was extracted from samples using the TRIzol method (Invitro Corp., Carlsbad, CA, USA).The RNA concentration and quality were assessed using a nanodrop and gelelectrophoresis. The samples were stored at ?80°C.
RNA sequencing was conducted by Novogene using an Illumina? (San Diego, CA, USA) based method to generate 20 million 150-bp paired-end reads per sample. The se-quencing library was prepared with the NEBNext? Ultra?RNA Library Prep Kit for Illumina?, and sequencing was performed on the NovaSeq PE150.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads stored in the fastq format after the Illumina sequencing were first pro-cessed through in-house perl scripts. In this step, clean reads were obtained by re-moving reads containing adapter, reads containing ploy-N, and low quality reads from the raw data. Clean reads were generated with high quality that were assessed by pa-rameters of the Q20, Q30, and GC contents.
Assembly: Botrytis cinerea B05.10 reference genome (GenBank accession number: GCA_000143535.4)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Dec 24, 2022 |
| Last update date |
Dec 12, 2023 |
| Contact name |
Xuncheng Wang |
| E-mail(s) |
1706380435@pku.edu.cn
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| Organization name |
Peiking University
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| Street address |
5 Yiheyuan Road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL32786 |
| Series (1) |
| GSE221721 |
Transcriptomic analysis of resistant and wild-type Botrytis ci-nerea isolates revealed fludioxonil-resistant mechanisms |
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| Relations |
| BioSample |
SAMN32398583 |
| SRA |
SRX18847354 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6893731_SI_4h3.FPKM.txt.gz |
97.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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