Dataset: Evolution of copper tolerance in the coastal diatom Skeletonema marinoi

SND-ID: 2023-47-1. Version: 1. DOI: https://doi.org/10.5878/7eww-g857

Citation

Alternative title

Live2tell

Creator/Principal investigator(s)

Björn Andersson - University of Gothenburg, Department of Marine Sciences orcid

Research principal

University of Gothenburg - Department of Marine Sciences rorId

Description

This project explores if, and how, contemporary populations the costal diatom Skeletonema marinoi have evolved in response to mining pollution. The study systems are two semi-enclosed inlets in the Baltic Sea, where one, Gåsfjärden (VG: 57°34.35'N, 16°34.98'E), has been affected by mining pollution for ca. 400 years, while the other, Gropviken (GP: 58°19.92N 16°42.35'E), has not. Strains were isolated, and the genome sequenced for 55 individual strains, and they were phenotyped in terms of specific growth rate and dose-responses to toxic copper concentrations (6-12 uM Cu). An artificial evolution experiment was conducted by assembling 28 and 30 strains from the two locations separately, and let them evolve with, and without, toxic Cu stress of 8.65 uM, corresponding to the concentration that inhibits the reference S. marinoi strain RO5AC’s specific growth rate with 50% in acute toxic tests (Andersson et al. 2020: DOI: 10.1016/j.aquatox.2020.105551). A recently developed 523 bp long strain-specific metabarcoding loci (*Sm_C12W1*: https://github.com/topel-research-group/Live2Tell) was used to tr

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This project explores if, and how, contemporary populations the costal diatom Skeletonema marinoi have evolved in response to mining pollution. The study systems are two semi-enclosed inlets in the Baltic Sea, where one, Gåsfjärden (VG: 57°34.35'N, 16°34.98'E), has been affected by mining pollution for ca. 400 years, while the other, Gropviken (GP: 58°19.92N 16°42.35'E), has not. Strains were isolated, and the genome sequenced for 55 individual strains, and they were phenotyped in terms of specific growth rate and dose-responses to toxic copper concentrations (6-12 uM Cu). An artificial evolution experiment was conducted by assembling 28 and 30 strains from the two locations separately, and let them evolve with, and without, toxic Cu stress of 8.65 uM, corresponding to the concentration that inhibits the reference S. marinoi strain RO5AC’s specific growth rate with 50% in acute toxic tests (Andersson et al. 2020: DOI: 10.1016/j.aquatox.2020.105551). A recently developed 523 bp long strain-specific metabarcoding loci (*Sm_C12W1*: https://github.com/topel-research-group/Live2Tell) was used to track the selection process. This locus is located on contig 12 of S. marinoi, inside a pentatricopeptide (PPR) repeat region of gene Sm_t00009768-RA, encoding an RNA-binding protein. The locus has 38 SNP positions amongst the 58 strains used in this study, and 110 unique alleles with 100% heterozygosity, including two triploid/aneuploid strains. The outcome was contrasted against strain selection models computed according to Andersson et al. 2022 (DOI: 10.1038/s41396-021-01092-9). The data and analyses included here are raw data and R-scripts that analyses the data, together with essential data created from the analysis. However, sequencing data is not processed or included, but has been deposited and available at NCBI under BioProject PRJNA939970. The amplicon sequencing data has been analyzed as outlined in https://github.com/topel-research-group/Bamboozle/wiki/Bamboozle-Part-2:-Barcode-Quantification. For more detailed information, see README.md files associated with each step of the analysis briefly outlined below. Each of the four sections includes necessary input data and can be run separately.

Barcodes
This is an analysis pipeline of the amplicon sequences of the selection experiment using the hypervariable locus in S. marinoi. The locus was bioinformatically identified based on analysis of whole genome sequences of 55 strains of S. marinoi from two Baltic Sea locations. It was predicted to have at least one unique allele enabling tracking of evolution through selection on standing genetic diversity in a artificial evolution experiment (See Fig above). Two barcode loci (Sm_C2W24 and Sm_C12W1) were sequenced in the experiment, but Sm_C12W1 had much more allelic diversity so the majority of the analysis focus on this data (see Barcodes/Barcoding_C12W1/README.md for more information). This Git repository does not contain the bioinformatic sequence analyses, but starts after raw reads have been trimmed, merged, and mapped back to the known allele sequences. Data from two pre-processing approaches are included, one based on Dada2 error-correction (Barcodes/Barcoding_C12W1/C12W1_BBmergeDada2_input), and one that uses exact matches of merged amplicon sequences (Barcodes/Barcoding_C12W1/ C12W1_abundances). The latter is the one we use for the publication: Andersson et al. Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi, in prep. for Molecular Ecology.

The zipfile Cu_evolution.zip contains all raw data, indexing information, R-scripts, and README.md files to reproduce the analysis and plot data. The documentation file README.md summarizes the contents of CU_evolution.zip. Key data from the analysis is provided as individual files, which are summarized in the documentation file Datafile_descriptions.md Show less..

Data contains personal data

No

Language

Method and outcome

Time period(s) investigated

2018-09-28 – 2023-02-20

Data format / data structure

Species and taxons

Skeletonema marinoi

Data collection
Geographic coverage

Geographic spread

Geographic location: Baltic Sea

Geographic description: The study includes two inlets located on the Swedish east-coast of the Baltic Sea. Between the 27-28th of June 2017 sediments from two semi-enclosed inlets, Gropviken (GP17; 58°19.92N 16°42.35'E) and Gåsfjärden (VG17; 57°34.35'N 16°34.98'E), were sampled. Gåsfjärden has been exposed to varying mining activity from the Solstad copper mine from the 17th to the early 20th century.

Administrative information

Responsible department/unit

Department of Marine Sciences

Other research principals

Contributor(s)

Olga Kourtchenko - University of Gothenburg, Department of Marine Sciences

Anna Godhe - University of Gothenburg, Department of Marine Sciences

Olof Berglund - Lund University, Department of Biology orcid

Helena L. Filipsson - Lund University, Department of Geology orcid

Kerstin Johannesson - University of Gothenburg, Department of Marine Sciences orcid

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Olga Kourtchenko - University of Gothenburg, Department of Marine Sciences

Anna Godhe - University of Gothenburg, Department of Marine Sciences

Olof Berglund - Lund University, Department of Biology orcid

Helena L. Filipsson - Lund University, Department of Geology orcid

Kerstin Johannesson - University of Gothenburg, Department of Marine Sciences orcid

Mats Töpel - IVL Swedish Environmental Research Institute orcid

Matthew I M Pinder - University of Gothenburg, Department of Marine Sciences orcid

Lara Hoepfner - University of Münster, Institute of Plant Biology and Biotechnology orcid

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Funding 1

  • Funding agency: Oscar and Lili Lamm Foundation rorId
  • Funding agency's reference number: FO2018-0042
  • Project name on the application: Framtidens landskap är beroende av sina samhällen – hur anpassas ett växtplanktonsamhälle till metall

Funding 2

  • Funding agency: Swedish Research Council for Environment Agricultural Sciences and Spatial Planning (FORMAS) rorId
  • Funding agency's reference number: 2016-00594
  • Project name on the application: Sedimentet berättar: Hur har växtplankton anpassats till miljögifter under de senaste 150 åren
Topic and keywords

Research area

Environmental sciences (Standard för svensk indelning av forskningsämnen 2011)

Microbiology (Standard för svensk indelning av forskningsämnen 2011)

Genetics (Standard för svensk indelning av forskningsämnen 2011)

Publications

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Andersson, B., Berglund, O., Filipsson, H. L., Kourtchenko, O., Godhe, A., Johannesson, K., Töpel, M., Pinder, M. I. M., Hoepfner, L., & Rengefors, K. (2023). Strain-specific metabarcoding reveals rapid evolution of copper tolerance in populations of the coastal diatom Skeletonema marinoi. Molecular Ecology, online ahead of print 2023-09-11.
DOI: https://doi.org/10.1111/mec.17116

Pinder, M. I. M., Andersson, B., Rengefors, K., Blossom, H., Svensson, M. & Töpel, M. (2023). Bamboozle: A bioinformatic tool for identification and quantification of intraspecific barcodes. bioRxkiv. Version 2, 2023-04-13.
DOI: https://doi.org/10.1101/2023.03.16.532925

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Published: 2023-07-04
Last updated: 2023-09-26