DOI: 10.5281/zenodo.15593805
title: Collection and Sequencing of Norwegian populations of Arabidopsis thaliana

description: Introduction

Arabidopsis thaliana is a widespread annual species with a range spanning from the tropics to north of the arctic circle. Previous research has shown local adaptation between populations sampled at large (Ågren and Schemske 2012; Ågren et al. 2013; Price et al. 2018) and small spatial scales. To date, much inference has been made by treating single accessions from nearby locations as populations. Here we conduct a proper sampling of both within and among population samples. Such data allow estimates of the frequencies of various types of polymorphism within populations.

Results

We sequenced 61 individuals of A. thaliana from across 12 natural populations in Norway. 

 








Sample ID



Country



Year



Lat



Long





NOR_2009_man1_1



Norway



2009



58.00



7.58





NOR_2009_man1_11



Norway



2009



58.00



7.58





NOR_2009_man1_16



Norway



2009



58.00



7.58





NOR_2009_man1_17



Norway



2009



58.00



7.58





NOR_2009_man1_4



Norway



2009



58.00



7.58





NOR_2009_man1_6



Norway



2009



58.00



7.58





NOR_2010_batn_10



Norway



2010



62.93



7.70





NOR_2010_batn_14



Norway



2010



62.93



7.70





NOR_2010_batn_15



Norway



2010



62.93



7.70





NOR_2010_batn_3



Norway



2010



62.93



7.70





NOR_2010_batn_6



Norway



2010



62.93



7.70





NOR_2010_flek_14



Norway



2010



58.40



6.62





NOR_2010_flek_19



Norway



2010



58.40



6.62





NOR_2010_flek_20



Norway



2010



58.40



6.62





NOR_2010_flek_3



Norway



2010



58.40



6.62





NOR_2010_flek_8



Norway



2010



58.40



6.62





NOR_2010_flek_9



Norway



2010



58.40



6.62





NOR_2010_haug_1



Norway



2010



63.38



10.07





NOR_2010_haug_12



Norway



2010



63.38



10.07





NOR_2010_haug_14



Norway



2010



63.38



10.07





NOR_2010_haug_4



Norway



2010



63.38



10.07





NOR_2010_hove_11



Norway



2010



63.37



10.07





NOR_2010_hove_12



Norway



2010



63.37



10.07





NOR_2010_hove_5



Norway



2010



63.37



10.07





NOR_2010_innf_10



Norway



2010



62.50



7.55





NOR_2010_innf_4



Norway



2010



62.50



7.55





NOR_2010_innf_6



Norway



2010



62.50



7.55





NOR_2010_larv_12



Norway



2010



59.10



10.10





NOR_2010_larv_15



Norway



2011



59.10



10.10





NOR_2010_larv_18



Norway



2012



59.10



10.10





NOR_2010_larv_3



Norway



2013



59.10



10.10





NOR_2010_larv_5



Norway



2014



59.10



10.10





NOR_2010_larv_9



Norway



2015



59.10



10.10





NOR_2010_orn1_17_S217



Norway



2010



66.88



13.70





NOR_2010_orn1_19_S218



Norway



2010



66.88



13.70





NOR_2010_orn1_4_S219



Norway



2010



66.88



13.70





NOR_2010_orn1_6_S220



Norway



2010



66.88



13.70





NOR_2010_orn1_8_S221



Norway



2010



66.88



13.70





NOR_2010_orn1_9_S222



Norway



2010



66.88



13.70





NOR_2010_rygg_1_S282



Norway



2010



59.38



10.77





NOR_2010_rygg_10_S283



Norway



2010



59.38



10.77





NOR_2010_rygg_16_S284



Norway



2010



59.38



10.77





NOR_2010_rygg_18_S285



Norway



2010



59.38



10.77





NOR_2010_rygg_5_S286



Norway



2010



59.38



10.77





NOR_2010_rygg_8_S287



Norway



2010



59.38



10.77





NOR_2010_sjo1_13_S301



Norway



2010



62.48



6.80





NOR_2010_sjo1_2_S303



Norway



2010



62.48



6.80





NOR_2010_sjo1_21_S304



Norway



2010



62.48



6.80





NOR_2010_sjo1_9_S305



Norway



2010



62.48



6.80





NOR_2010_skat_13_S306



Norway



2010



63.50



10.80





NOR_2010_skat_14_S307



Norway



2010



63.50



10.80





NOR_2010_skat_17_S308



Norway



2010



63.50



10.80





NOR_2010_skat_3_S309



Norway



2010



63.50



10.80





NOR_2010_skat_4_S310



Norway



2010



63.50



10.80





NOR_2010_skat_9_S311



Norway



2010



63.50



10.80





NOR_2010_thei_10_S336



Norway



2010



63.43



10.42





NOR_2010_thei_12_S337



Norway



2010



63.43



10.42





NOR_2010_thei_18_S338



Norway



2010



63.43



10.42





NOR_2010_thei_21_S339



Norway



2010



63.43



10.42





NOR_2010_thei_4_S340



Norway



2010



63.43



10.42





NOR_2010_thei_7_S341



Norway



2010



63.43



10.42






 

Table 1 provides the sample ID, Country, Year of Collection, Latitude and longitude of each sample.

Materials and Methods

We collect and sequenced Arabidopsis thaliana populations from southernmost Norway to north of the Arctic circle (latitude >68º N). In each of 12 populations, seeds were collected from 12-48 replicate maternal plants. These collections were made in 2009 and 2010 and are described in detail by Oakley et al. (2019). From each of the 12 populations between 3 and 6 individual plants were propagated single seed descent in a growth chamber at Purdue University (each plant representing a different maternal family collected in the field; a total of 61 lineages). 

DNA Extraction, Library Preparation, and Whole Genome Sequencing

To obtain plant tissue for DNA extraction, seeds from each of the 61 lineages were sown in the Colorado State University greenhouse. A single plant was sampled from each family once plants reached the vegetative state, and leaf tissue from that plant was used for subsequent DNA extraction using the Qiagen DNeasy Plant Mini Kit (Valencia CA, USA). Extracted DNA was then quantified using a Qubit Fluorometer (ThermoFisher Scientific). Whole genome sequencing (WGS) libraries of the extracted DNA were prepared at the University of Colorado Boulder sequencing core. These WGS libraries were then paired-end (2 x 150 base pairs) whole genome sequenced at the University of Colorado Anschutz Medical Campus using an Illumina NovaSeq 6000. Sequencing efforts aimed for 30x coverage of the Arabidopsis thaliana genome.

Raw WGS Read QC and Alignment Processing

Raw sequence data were evaluated with FastQWC (Andrews 2010, version 0.11.8) to assess read quality and adapter contamination. Trimmomatic (Bolger et al. 2014, version 0.39) was then used with default parameters to remove low-quality reads and any adapter contamination identified in the FastQC report. The trimmed sequence reads were then aligned to version 10 of the Colombia reference genome (GenBank assembly accession ID = GCA_000001735.1) using BWA-MEM with default settings (Li 2013, version 0.7.17). Samtools (Li et al. 2009, version 1.9) was then used to sort sequence alignment files, mark duplicate reads, keep only properly paired reads and remove reads with a mapping quality less than 10. 

 

 

Acknowledgements

Sequencing of Norwegian accessions was supported by NSF DEB-1743273 to CGO and JKM.

 

References

Ågren, J., and D. W. Schemske. 2012. Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range. New Phytologist 194:1112-1122. https://doi.org/10.1111/j.1469-8137.2012.04112.x 

 

Ågren, J., CG Oakley, JK McKay, JT Lovell, DW Schemske. 2013. Genetic mapping of adaptation reveals fitness trade-offs in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 110: 21077-21082 https://doi.org/10.1073/pnas.1316773110.

 

Andrews, S. (2010). FastQC. Babraham Bioinformatics. https://doi.org/citeulike-article-id:11583827 

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btu170 

 Li, H. (2013). [Heng Li - Compares BWA to other long read aligners like CUSHAW2] Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv Preprint ArXiv. 

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp352 

 Oakley, CG, Lundemo S, Ågren J, Schemske DW. 2019. Heterosis is common and inbreeding depression is absent in natural populations of Arabidopsis thaliana. Journal of Evolutionary Biology 32:592–603. https://doi.org/10.1111/jeb.13441  

N Price, BT Moyers, L Lopez, JR Lasky,  JG Monroe, JL Mullen, CG Oakley, J Lin, J Ågren, DR Schrider, AD Kern, JK McKay. 2018. Combining population genomics and fitness QTL to identify the genetics of local adaptation in Arabidopsis thaliana. Proceedings of the National Academy of Sciences, https://doi.org/10.1073/pnas.1719998115