Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe - ITS1 dataset

Description of the data and file structure

We genotyped the ITS1 locus of 178 herbarium specimens using protocol described in Suchan et al. (2018; https://doi.org/10.1111/1755-0998.12948) and processed using custom script. The specimens were chosen after morphological determination of their cytotypes (morphological determination accuracy: 97.8%). We choose this subsample (3.5% of the total number of specimens) to represent comparable distributional ranges and collection dates across both cytotypes, including specimens from both the native and expanded ranges of tetraploid C. stoebe. Genotyping of the ITS1 locus unambiguously identifies the cytotype, as all tetraploid samples exhibit a unique ribotype B, which has never been found in diploid samples (Mráz et al., 2012; https://doi.org/10.1016/j.ympev.2011.11.006).

Files and variables

File: Centaurea_stoebe_ITS1_script.sh

Description: This file contains the script used for processing raw sequence data to obtain a table with the numbers of reads in each sample mapping to the obtained ITS1 variants. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.1

File: Centaurea_stoebe_sample_list.xlsx

Description: This file contains a list of analyzed herbarium specimens.

Variables

ID - sample ID

Lab working no. - Identifier of the samples in the ITS1 analyses, specifically in the Centaurea_stoebe_ITS1_sequence_numbers.xlsx file

Morphology-based estimation - ploidy of the sample estimated with morphology (2 - diploid, 4 - tetraploid)

ITS seq based estimation - ploidy of the sample estimated using ITS1 sequencing (2 - diploid, 4 - tetraploid)

Congruence(1)/mismatch(0) - congruence (1) or mismatch (0) between morphological and genetic policy estimation

Country of origin

Herbarium

Herbarium coll. number

Collector

Collection year

Locality

Latitude

Longitude

File: Centaurea_stoebe_ITS1_sequences.fasta

Description: This file contains sequences of the obtained ITS1 variants.

File: Centaurea_stoebe_ITS1_sequence_numbers.xlsx

Description: This file contains a table with the numbers of reads in each sample mapping to the obtained ITS1 variants.

Variables

OTU - ITS1 variant number

size - number of sequences from the total data clustered to the variant

next columns contain numbers of reads mapped to each ITS1 variant for each sample

Code/software

The code to process sequence data is included in Centaurea_stoebe_ITS1_script.sh file. The software used was: PEAR v0.9.6, cutadapt v.3.2, vsearch v2.28.