Scripts for bioinformatics processing and analysis for Zostera marina poolseq project.
Contact: nick.jeffery@dfo-mpo.gc.ca
Citation: Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor M, Wong M. 2024. Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina). Published online at Evolutionary Applications
We used a pooled-sequencing approach for 23 eelgrass populations (geographic locations) and aligned reads generated by a NovaSeq platform to a publicly available Zostera marina genome assembly (Ma et al. 2021).
Raw sequence reads for each pool are deposited in the NCBI Sequence Read Archive at https://www.ncbi.nlm.nih.gov/sra/PRJNA891275.
The scripts here include trimming reads with fastp, alignment to the reference genome using bwa-mem2, removal of duplicate reads and indel realignment using GATK, and conversion of binary alignment files to mpileup format, and then sync format for Popoolation2.
Post-bioinformatics analyses conducted in BayPass (Gautier 2015), Treemix (Pickrell and Pritchard 2012), and the R package poolfstat (Gautier et al. 2021).
#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq
Chr01 1 42612672 25740331 42520710 99.7842 87.0496 35.6 49.7
Chr02 1 40099171 21866617 39942582 99.6095 78.4374 35.6 40.2
Chr03 1 39935026 25496738 39351073 98.5377 91.5507 35.6 42
Chr04 1 34618966 22617769 34451221 99.5155 93.9099 35.6 41
Chr05 1 32617008 19391682 32516701 99.6925 85.7323 35.6 48.8
Chr06 1 29411071 17365610 29250779 99.455 85.1597 35.6 49.5
Running a PCA on ~500,000 SNPs across all 23 sites results in a division along PC1 between Atlantic and Pacific sites, while PC2 shows a latitudinal gradient in population structure among Atlantic and subarctic sites
The authors wish to thank numerous collaborators that helped collect or provided eelgrass samples, including Tim Bernard, Isabelle Berube, Renee Bernier, Veronika Brzeski, Mike Coffin, Phil Colarusso, Chantal Coomber, Tessa Craig, France Dufresne, Coady Fitzpatrick, Robert Gregory, Javier Guijarro-Sabaniel, Cynthia Hays, Frederica Jacks, Kira Krumhansl, Andre Nadeau, John O’Brien, Shawn Roach, Stephanie-Robertson Kempton, Nathalie Simard, Sandrine Tousignant and Erica Watson, as well as Zeliang Wang and Dave Brickman for providing outputs from the BNAM oceanographic model. Kara Layton, Sarah Lehnert, Brenna Forester, and Thibaut Capblancq provided advice on conducting genomic offset analyses. We also thank the staff and technical personnel at Génome Québec for DNA extraction and sequencing.