This readme file was generated on 2026-05-19 by Kinga Stolarek and provides a list and description of each file included in the dataset.

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DATASET GENERAL INFORMATION
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Title of dataset: Diversity and composition of the seed-associated mycobiome of silver birch (Betula pendula Roth) in Sweden
Creator(s)/Primary investigator(s): Kinga Stolarek, ORCID 0009-0009-4165-3597
Persistent identifier of dataset: https://doi.org/10.5878/z8wq-5q93
Related publication for description of project, methods etc: Kinga Stolarek, Dušan Sadiković, Michelle Cleary. "Diversity and composition of the seed-associated mycobiome of silver birch (Betula pendula Roth) in Sweden", Mycological Progress, submitted.


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FILE OVERVIEW
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"Amplicon_sequencing_data.tsv.txt"

Brief description of content: The fungal communities of empty and filled seeds from seven seed lots collected in southern Sweden were assessed using DNA amplicon sequencing. 

"Traditional_culturing_data.tsv.txt"

Brief description of content: The fungal communities of empty and filled seeds from seven seed lots collected in southern Sweden were assessed using Traditional in-vitro culturing with Sanger sequencing and phylogenetic analyses. The file contains information on fungal taxa identified at the genus and species levels. 


Seeds of silver birch were collected during September 2023 from ten sources in southern Sweden, comprising eight open pollinated stands and two seed orchards (i.e., Ekebo, Remningstorp, Skåne, Falkenberg, Skåne 2, Skåne 3, Skåne 4, Göteborg, Vimmerby, Värnamo; Fig. S1). After collection, seeds were stored at room temperature until further processing. Before fungal analyses, seeds were: cleaned of scales, de-winged and separated into two groups based on embryo presence: filled seeds or empty seeds and surface-sterilized. 
Location coordinates: 
55.95054, 13.11244 - Ekebo 
58.449511, 13.645254,- Remningstorp 
55.577039, 13.318768,- Skåne 1
56.910468, 12.602582,- Falkenberg 
55.723310, 13.967567,- Skåne 2
55.644775, 13.598644,- Skåne 3 
55.581479, 13.408102,- Skåne 4
57.8696496, 11.9388275,-Göteborg 
57.6041921, 15.7911998,-Vimmerby
57.143998, 13.967921 -Värnamo


Relationship between files: The datasets were generated from the same seed material but were analysed and interpreted separately due to the use of two different methodological approaches for fungal identification

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DATA-SPECIFIC INFORMATION FOR "Amplicon_sequencing_data.tsv.txt"
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License: Creative Commons Public Domain Dedication CC0

Number of columns/variables:22

Number of rows/cases: 804

Codes for missing or empty data: missing data = NA

Variable list:  
-ASV: Amplicon sequence variants (ASVs) were generated and taxonomically assigned against the UNITE reference database (https://unite.ut.ee/) using QIIME2 (v2022.2). To improve taxonomic resolution, ASVs not classified beyond the class level using the UNITE database were queried against the NCBI GenBank database using BLASTn. Only best hits with ≥94% sequence identity were retained for genus-level classification. 
-EkF: Information about location "EK" - "Ekebo" and type of seed "F" - "Filled (with embryo)" and number of reads; respectively below: 
-EkE	"EK" - "Ekebo" and type of seed "E" - "Empty (no embryo)"
-ReF	"Re" - "Remningstorp" and type of seed "F" - "Filled (with embryo)"
-ReE	"Re" - "Remningstorp" and type of seed "E" - "Empty (no embryo)"
-Sk1F	"Sk1" - "Skane 1" and type of seed "F" - "Filled (with embryo)"
-Sk1E	"Sk1" - "Skane 1" and type of seed "E" - "Empty (no embryo)"
-Sk2F	"Sk2" - "Skane 2" and type of seed "F" - "Filled (with embryo)"
-Sk2E	"Sk2" - "Skane 2" and type of seed "E" - "Empty (no embryo)"
-GoF	"Go" - "Goteborg" and type of seed "F" - "Filled (with embryo)"
-GoE	"Go" - "Goteborg" and type of seed "E" - "Empty (no embryo)"
-ViF	"Vi" - "Vimmerby " and type of seed "F" - "Filled (with embryo)"
-ViE	"Vi" - "Vimmerby " and type of seed "E" - "Empty (no embryo)"
-FaF	"Fa" - "Falkenberg" and type of seed "F" - "Filled (with embryo)"
-FaE    "Fa" - "Falkenberg" and type of seed "E" - "Empty (no embryo)"
-Percent_Identity- Percentage sequence similarity between the ASV and the best matching reference sequence obtained using BLASTn against the NCBI GenBank database.	
-Kingdom - Organism classification at the kingdom taxonomic rank.	
-Phylum	- Organism classification at the phylum taxonomic rank.
-Class	- Organism classification at the class taxonomic rank.
-Order	- Organism classification at the order taxonomic rank.
-Family	- Organism classification at the family taxonomic rank.
-Genus - Organism classification at the genus taxonomic rank.



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DATA-SPECIFIC INFORMATION FOR "Traditional_culturing.tsv.txt"
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License: Creative Commons Public Domain Dedication CC0

Number of columns/variables: 11

Number of rows/cases: 140

Codes for missing or empty data: missing data = Blank space

Variable list:  
Location: Seed lot origin/location where samples were collected such as: Remningstorp, Skåne, Falkenberg, Skåne 2, Skåne 4, Göteborg, Vimmerby	
Sample: Sample identifier containing information about seed lot origin and seed type. Location abbreviations consist of the first two letters of the location name (plus a number when applicable). Seed type abbreviations: E = empty seed (without embryo), F = filled seed (with embryo).
Seed_type: Empty (no embryo) and Filled (with embryo)
Plate, Isolate, Morphotype - indicating order in culture collection preserved in SLU Alnarp. 	
DNA - Indicates whether the isolate was selected as a representative for DNA sequencing (yes/no).
Genus - Organism classification at the genus taxonomic rank.
Species	- Organism classification at the species taxonomic rank.
NCBI_culture_name — Identifier used for sequence submission and search in the NCBI database and for reference in the culture collection preserved at SLU Alnarp.
ITS_accession_number — ITS sequence accession number assigned by NCBI GenBank.



