This readme file was generated on 2026-02-17 by Polona Kogovšek

# GENERAL INFORMATION

* Title of Dataset: Data from qPCR analysis of air and rainwater samples: Analysis of plant and environmental samples for the quarantine fungus Phyllosticta citricarpa in four European citrus-growing areas

## Author/Principal Investigator Information
Name: Polona Kogovšek
ORCID:0000-0002-4035-0115
Institution: National Institute of Biology
Address: Večna pot 121, 1000 Ljubljana 
Email: Polona.kogovsek@nib.si

## Author/Associate or Co-investigator Information
Name: Irene Vloutoglou 
ORCID: 0000-0003-2886-1200
Institution: Benaki Phytopathological Institute (BPI)
Address: 8 Stefanou Delta street, 145 61 Kifissia, Attica, Greece
Email: i.vloutoglou@bpi.gr


* Date of data collection: 2018 - 2021
* Geographic location of data collection: Greece, Italy, island of Malta, Island of Gozo (Malta)
* Information about funding sources that supported the collection of the data: European Food Safety Authority (SMART Surveillance, GP/EFSA/AFSCO/2017/04) and the Slovenian Research Agency programmes P4-0463 and P4-0431.


# SHARING/ACCESS INFORMATION

* Licenses/restrictions placed on the data: CC-BY
* Links to publications that cite or use the data: 10.1111/aab.70112
* Links to other publicly accessible locations of the data: /
* Links/relationships to ancillary data sets: /
* Was data derived from another source? no
	* If yes, list source(s): /
* Recommended citation for this dataset: 


# DATA & FILE OVERVIEW

## File List: *list all files (or folders, as appropriate for dataset organization) contained in the dataset, with a brief description*

* Relationship between files, if important: One excel file with two sheets
* Additional related data collected that was not included in the current data package: no 
* Are there multiple versions of the dataset? no
	* If yes, name of file(s) that was updated: /
	* Why was the file updated? /
	* When was the file updated? /


# METHODOLOGICAL INFORMATION

## Description of methods used for collection/generation of data: 
Three qPCR assays were used to test DNA extracted from air and rainwater samples: (i) the PC assay (Van Gent-Pelzer et al., 2007), (ii) the PC-2 assays (Schirmacher et al., 2019) and (iii) the Pc-TEF1 assay (Zajc et al., 2023). All air and rainwater DNA samples were tested using the PC-2 and Pc-TEF1 assays, with the majority also tested with the PC assay, except for samples IAS2 to IAS18, MAS1 to MAS81, GRW1 to GRW6 and IRW1 to IRW5. Three control qPCR assays targeting eukaryotic or fungal DNA were used as well: (i) the Yeast assay (Hierro et al., 2006) targeting fungal DNA was used to test 51 air samples (i.e., IAS2 to IAS19 and MAS1 to MAS30), (ii) the Eukaryotic 18S rRNA Endogenous Control (4319413E; Applied Biosystems, Foster City, California, United States), targeting all eukaryotic DNA, was used to test the remaining 268 air samples and all the rainwater samples, and (iii) the broad-range FungiQuant (FQ) assay (Liu et al., 2012) was used to test all air and rainwater samples. Each DNA sample was diluted 10-fold in molecular grade water and tested in three technical replicates using qPCR.
 

## Methods for processing the data: 
The obtained Cq values were analysed in Microsoft Excel, where average Cq values and standard deviation of the three technical replicates were calculated. For ease of presentation, results obtained with the Yeast assay (48 air samples) were interpreted together with the 18S rRNA results.

## Instrument- or software-specific information needed to interpret the data: 
n.a.

*include any additional methodological information needed to interpret and/or use the data, as appropriate*
* Standards and calibration information, if appropriate: 
* Environmental/experimental conditions: 
Except for the FQ and Yeast assays, qPCR reactions for all assays consisted of 1x TaqMan Universal PCR Master Mix (Applied Biosystems), 300 nM of each primer, 200 nM TaqMan probe and 2 µl of DNA sample in a total volume of 10 µl. For the FQ assay, the reaction consisted of 1x Quantabio PerfeCTa qPCR ToughMix Low ROX (Quantabio, Beverly, Massachusetts, United States), 900 nM of each primer and 250 nM TaqMan probe. The reaction mixture for the Yeast assay consisted of SYBR Green PCR Master Mix (Applied Biosystems) and 200 nM of each primer. The following cycling conditions were applied for all reactions: 2 min at 50 °C for UNG treatment, 10 min at 95 °C for Taq polymerase activation, followed by 45 cycles of 95 °C for 15 s for denaturation and 60 °C for 1 min for annealing and extension. For reactions using SYBR Green chemistry, the dissociation curve was carried out at the end of the qPCR amplification, and the melting temperature (Tm) of the amplified product was checked. Fluorescence was measured after each annealing/elongation step, and the threshold value was adjusted manually. qPCR analyses were performed using an ABI PRISM 7900 Sequence Detector or an ABI PRISM ViiA7 (Applied Biosystems).
* Describe any quality-assurance procedures performed on the data: 
In each qPCR run, a positive control (DNA of P. citricarpa strain CBS 127451) and a negative control (nuclease-free water) were included and results were verified before proceeding with the analysis of individual samples.

* People involved with sample collection, processing, analysis and/or submission: 
Vloutoglou, I., Kogovšek, P., Bergamaschi, V., Boonham, N., Ferle, M., Fišer, S., Kalogeropoulou, E., Kampletsas, A., Kogej Zwitter, Z., Ligka, A., Macarthur, R., Pirone, L., Ravnikar, M., Riccioni, L., Valente, M. T., Vella, D., Zajc Žunič, J., & Vicent, A.

# DATA-SPECIFIC INFORMATION FOR: spreadsheet Air
* Number of variables: 15
* Number of cases/rows: 319
* Variable List: Sampling site; Sampling start date; Sampling end date; DNA Sample Code; Date of DNA extraction; 18S rRNA/Yeast (Cq); 18S rRNA/Yeast (StDev); 18S rRNA/Yeast (NoP); Yeast (Tm); FQ (Cq); FQ (StDev); FQ (NoP); PC; PC-2; Pc-TEF1
* Missing data codes: n.a.
* Specialized formats or other abbreviations used: /

# DATA-SPECIFIC INFORMATION FOR: spreadsheet Rainwater
* Number of variables: 13
* Number of cases/rows: 306
* Variable List: Sampling site; Sampling date; DNA Sample Code; Date of DNA extraction; 18S rRNA (Cq); 18S rRNA (StDev); 18S rRNA (NoP); FQ (Cq); FQ (StDev); FQ (NoP); PC; PC-2; Pc-TEF1
* Missing data codes: n.a.
* Specialized formats or other abbreviations used: /