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| Status |
Public on Feb 15, 2024 |
| Title |
VF_3 |
| Sample type |
SRA |
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| Source name |
whole animal from laboratory colony
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| Organism |
Planococcus citri |
| Characteristics |
developmental stage: adult
status: virgin
Sex: female
tissue: whole animal
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| Treatment protocol |
Mated females were collected from the main P. citri stock colony described in the rearing protocol. These were collected after checking for the presence of ovisacs with fertilized eggs, which means that females were effectively mated. Virgin females were obtained as described in Vacas et al (2019). New lemons infested with P. citri first instars from the main stock colony were maintained in different plastic boxes. After the second instar stage, males produce a cottony cocoon that covers their bodies to pupate. Then, those lemons were periodically checked for the presence of cocoons, which were manually removed with an entomological needle to avoid matings and leave lemons infested only with virgin females.
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| Growth protocol |
The colony of Planococcus citri was established at the Universitat Politècnica de València (UPV, Valencia, Spain) using starting specimens from Servicio de Sanitat Vegetal (Generalitat Valenciana, Silla, Valencia, Spain). Mealybugs were reared on organic green lemons. These were previously covered with paraffin around the midsection to delay their desiccation. Insects were maintained in a rearing chamber (darkness, at 24 ± 2 °C and 40−60% relative humidity) in plastic boxes.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol total RNA extraction and DNase I treatment
Illumina TrueSeq RNA-Seq strand-specific library prep
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SAM44185
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| Data processing |
CLC Genomics Workbench 10.0.1 & FastQC & centrifuge, quality control
CLC Genomics Workbench 10.0.1, adapter and polyA tail trimming
CLC Genomics Workbench 10.0.1, mapping to the genome with 'RNA-Seq analysis' tool (parameters: Mismatch cost 2, Insertion cost 3, Deletion cost 3, Length fraction 0.9, Similarity fraction 0.9, Global alignment No, Auto-detect paired distances Yes, Strand specific Reverse, Maximum number of hits for a read 1, Count paired reads as two Yes, Expression value Unique counts) and export of 'Expression Browser' count table
R version 3.4.2 with packages edgeR_3.20.9, filtering genes with raw counts below 10 in less than 4 samples
R version 3.4.2 with packages edgeR_3.20.9, TMM normalization
R version 3.4.2 with packages limma_3.34.9, voom transformation, linear model fit, adj.p.val calculation (BH correction)with eBayes function, DE table export
Genome_build: Pcitri.v1 (draft genome available at request at ensembl.mealybug.org)
Supplementary_files_format_and_content: Pcitri_totalCounts.txt - table with raw gene counts for all genes and all samples
Supplementary_files_format_and_content: Pcitri_lcpm.txt - table with logCPM values for all genes and all samples
Supplementary_files_format_and_content: Pcitri_logFC_PAdj.xlsx - Differential gene expression table with logFC and adj.p.val for the comparison virgin vs mated females; includes InterPro domain gene annotations
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| Submission date |
Jul 07, 2021 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Marko Petek |
| E-mail(s) |
marko.petek@nib.si
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| Organization name |
National Institute of Biology
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| Department |
Department of Biotechnology and Systems Biology
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| Street address |
Večna pot 111
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| City |
Ljubljana |
| ZIP/Postal code |
1000 |
| Country |
Slovenia |
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| Platform ID |
GPL30369 |
| Series (1) |
| GSE179660 |
Planococcus citri mealybug virgin and mated female transcriptome sequencing |
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| Relations |
| BioSample |
SAMN20094147 |
| SRA |
SRX11370594 |
| 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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