Dataset DOI: https://doi.org/10.5061/dryad.wh70rxwzn

Description of the data and file structure

We present six high-quality, chromosome-scale genome assemblies for wild Salicornia species. The six genomes include diploids Salicornia brachiata (2n = 2x = 18), Salicornia sinus-persica (2n = 2x = 18), Salicornia europaea (Israel) (2n = 2x = 18) and Salicornia persica ssp. iranica (2n = 2x = 18) and allotetraploids Salicornia bigelovii (2n = 4x = 36), and Salicornia sp. France (2n = 4x = 36). These Salicornia genomes were sequenced using PacBio HiFi to an average depth of 73x (ranging from 28 x to 143 x) and chromatin confirmation sequencing (Omni-C with average coverage of 91x). The annotation file was generated using the BRAKER3 pipeline, incorporating transcript and protein sequences for gene model prediction.

We mapped all 318 accessions to an in silico octoploid reference assembly. This reference was constructed by merging two tetraploid assemblies Salicornia sp. France (4X) and S. bigelovii (4X) reported in this study.

File List and Descriptions

1. Genome assemblies and annotations (per species)

For each species/accession, four files are provided following the naming convention:

Where <Species_name> is one of:

• Salicornia_bigelovii (Salicornia bigelovii)
• Salicornia_brachiata (Salicornia brachiata)
• Salicornia_europaea_Israel (Salicornia europaea, Israel accession)
• Salicornia_persica_ssp_iranica (Salicornia persica ssp. iranica)
• Salicornia_sinus_persica (Salicornia sinus-persica)
• Salicornia_sp_France (Salicornia sp., France accession)

Complete list of the 24 files in this category:

• Salicornia_bigelovii.fasta.gz
• Salicornia_bigelovii.gff.gz
• Salicornia_bigelovii.cds.fa.gz
• Salicornia_bigelovii.protein.fa.gz
• Salicornia_brachiata.fasta.gz
• Salicornia_brachiata.gff.gz
• Salicornia_brachiata.cds.fa.gz
• Salicornia_brachiata.protein.fa.gz
• Salicornia_europaea_Israel.fasta.gz
• Salicornia_europaea_Israel.gff.gz
• Salicornia_europaea_Israel.cds.fa.gz
• Salicornia_europaea_Israel.protein.fa.gz
• Salicornia_persica_ssp_iranica.fasta.gz
• Salicornia_persica_ssp_iranica.gff.gz
• Salicornia_persica_ssp_iranica.cds.fa.gz
• Salicornia_persica_ssp_iranica.protein.fa.gz
• Salicornia_sinus_persica.fasta.gz
• Salicornia_sinus_persica.gff.gz
• Salicornia_sinus_persica.cds.fa.gz
• Salicornia_sinus_persica.protein.fa.gz
• Salicornia_sp_France.fasta.gz
• Salicornia_sp_France.gff.gz
• Salicornia_sp_France.cds.fa.gz
• Salicornia_sp_France.protein.fa.gz

2. Population genomics analysis results (VCF-based)

These files contain variant calls and summary statistics (nucleotide diversity π, Tajima's D, Fst). File names follow the convention:

<Sample/population>.sites.called.on.<Reference>_<window/region>_<statistics>.vcf[.zip]

where:

• <Sample/population> — the population analyzed: S_procumbens (S. procumbens) or S_sp.France (Salicornia sp. France); S_sp.France_S.procumbens indicates a pairwise comparison between the two populations.
• <Reference> — the reference genome used for variant calling: S.France.Ref (Salicornia sp. France assembly) or S.ramosissima.Ref (S. ramosissima assembly).
• <window/region> — 50kb.window_All.chr = statistics computed in 50-kb windows across all chromosomes; chr6A = analysis restricted to chromosome 6A.
• <statistics> — TajimaD.pi / tajimasD.pi = Tajima's D and nucleotide diversity (π); Fst = fixation index between populations.

Files in this category:

• S_procumbens.sites.called.on.S.France.Ref_50kb.window_All.chr.TajimaD.pi.vcf.zip — Sites of S. procumbens called against the Salicornia sp. France reference; Tajima's D and π in 50-kb windows, all chromosomes.
• S_procumbens.sites.called.on.S.ramosissima.Ref_input.tajimasD.pi.chr6A.vcf — Sites of S. procumbens called against the S. ramosissima reference; input for Tajima's D and π calculation on chromosome 6A.
• S_sp.France_S.procumbens_Chr6A.called.on.S.ramosissima_input.Fst.chr6A.vcf.zip — Joint variant calls of Salicornia sp. France and S. procumbens against the S. ramosissima reference; input for Fst calculation on chromosome 6A.
• S_sp.France.sites.called.on.S.France.Ref_50kb.window_All.chr.TAjimaD.pi.vcf.zip — Sites of Salicornia sp. France called against the Salicornia sp. France reference; Tajima's D and π in 50-kb windows, all chromosomes.
• S_sp.France.sites.called.on.S.ramosissima.Ref_input.tajimasD.pi.chr6A.vcf.zip — Sites of Salicornia sp. France called against the S. ramosissima reference; input for Tajima's D and π calculation on chromosome 6A.

3. Other files

• Genome.coverage.graph.zip — Genome coverage graph(s).
• vcf_MAF_Missing_Het_filter.pl — Perl script used to filter VCF files by minor allele frequency (MAF), missing-data rate, and heterozygosity.

Code/software

Contig level assemblies for six Salicornia species were generated by using hifiasm (v2.28) with default parameters. Each contigs of contig level assemblies were aligned with the NCBI Nucleotide database by blast. Contamination contigs and low quality contigs were removed by the result of blobtools (v1.1.1). Contaminated contigs are those identified based on alignment results as originating from contigs that do not belong to Streptophyta, while low-quality contigs are those with a relatively low average sequencing depth. For S. brachiata, S. sinus-persica, S. europaea (Israel), S. persica ssp. iranica, and S. bigelovii, contigs were anchored using Omni-C data with Juicer (v2.0). Omni-C contact maps were then generated using the 3d-dna pipeline (v180922), followed by manual inspection and correction using Juicebox (v2.17.00). Salicornia sp. France was scaffolded using the HapHic pipeline (v1.0.5) with default parameters. 

The resulting read-depth coverage plots enabled the assignment of accessions to specific subgenomes (A, B, C, and D). We followed the approach described in Adhikari, et al (2022) to generate read-depth coverage plots and confirm subgenomes and ploidy using the sequence data.

Access information

Other publicly accessible locations of the data:

• Genome assemblies of this project have been deposited at GenomeWarehouse in BIG Data Center under Project numbers PRJCA036664.

Data was derived from the following sources:

• The raw FASTQ files of the whole-genome sequencing panel of Salicornia accessions used in this study, along with Pacbio HiFi long reads, ISO-Seq and Omni-C, have been deposited at the National Center for Biotechnology Information under BioProject accession (PRJNA1247873).