Collection and Sequencing of Norwegian populations of Arabidopsis thaliana

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