Dataset: Sample collection and sequence accession information for Zostera marina whole genome resequencing from specimens collected at 16 geographic locations worldwide in 2017

We conducted a range-wide sampling collection of 190 Zostera marina specimens from 16 geographic locations (Yu et al. 2023 Nature Plants). The chosen populations feature a mix of sexual and vegetative reproduction with the exception of mostly vegetative reproduction at the sites PO and NN, apparent through extended clones. Chosen locations were a subset of the Zostera Experimental Network sites that were previously analysed using 24 microsatellite loci. Although a sampling distance of >2 meters was maintained to reduce the likelihood of collecting the same genet/clone twice, this was not always successful and thus provided an estimate of local clonal diversity. Plant tissue was selected from the basal meristematic part of the shoot after peeling away the leaf sheath to minimize epiphytes (bacteria and diatoms), frozen in liquid nitrogen and stored at -80 degrees Celsius (°C) until DNA extraction. Quality control was performed following Joint Genome Institute guidelines (https://jgi.doe.gov/wp-content/uploads/2013/11/Genomic-DNA-Sample-QC.pdf). Plate-based DNA library preparation for Illumina sequencing was performed on the PerkinElmer Sciclone NGS robotic liquid handling system using Kapa Biosystems library preparation kit. About 200 nanograms (ng) of sample DNA was sheared to a length of around 600 base pairs (bp) using a Covaris LE220 focused ultrasonicator. Selected fragments were end-repaired, A-tailed, and ligated with sequencing adaptors containing a unique molecular index barcode. Libraries were quantified using KAPA Biosystems' next-generation sequencing library qPCR-kit on a Roche LightCycler 480 real-time PCR instrument. Quantified libraries were then pooled together and prepared for sequencing on the Illumina HiSeq2500 sequencer using TruSeq SBS sequencing kits (v4) following a 2 × 150 bp indexed run recipe to a targeted depth of approximately 40x coverage. The quality of the raw reads was assessed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and visualized by MultiQC58. BBDuk (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) was used to remove adapters and for quality filtering, discarding sequence reads (1) with more than one 'N' (maxns = 1), (2) shorter than 50 bp after trimming (minlength = 50), and (3) with average quality <10 after trimming (maq = 10). FastQC and MultiQC were used for a second round of quality check for the clean reads. Sequencing coverage and mapping rate were calculated for each sample (see Yu et al. 2023 for details).