DOI: 10.5061/dryad.c866t1gk1
title: Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources

description: Background Human-induced habitat changes threaten biodiversity, prompting
 large-scale restoration initiatives. Revegetation through direct seeding
 is common in agricultural and infrastructure construction projects, yet
 the provenance of seed material and its genetic impacts on natural
 populations remain underexplored. Introducing foreign ecotypes can lead to
 unintended consequences, as they may be adapted to different environmental
 conditions or represent distinct evolutionary lineages. In Switzerland,
 direct seeding is widely used to promote dry meadows, often using seeds of
 the Carthusian pink (Dianthus carthusianorum). Results To assess the
 extent and genetic effects of direct seeding and infer seed provenances,
 we combined genomic data from 446 samples collected in independent,
 smaller-scale studies. We assembled a chromosome-level reference genome to
 map reads and developed a panel of 48,299 representative single nucleotide
 polymorphisms (SNPs). We identified six evolutionary significant units
 (ESUs) within the European distribution range of D. carthusianorum. As
 biodiversity promotion efforts are often coordinated nationally, we
 focused on populations in Switzerland, where we found five ESUs: four
 occur naturally, and one was introduced from Eastern Europe. Our combined
 genomic data revealed that 15 of 31 randomly sampled populations across
 Switzerland (48.4%) originated from direct seeding. Allochthonous seed
 material was detected in eight populations (25.8%), with six of these
 showing admixture involving two to three ESUs. Conclusions Our results
 demonstrate the effectiveness of genomic approaches for identifying direct
 seeding and clarifying seed provenance, thereby supporting decision-making
 in national revegetation projects and emphasising the importance of using
 autochthonous seed sources.
description: # Data from: Genomic identification of direct seeding and evolutionary
 lineages by combining heterogeneous genomic resources Dianthus
 carthusianorum Reference Genome
 (CARY_DIA_CAR_CH_CHANT_001_HiFi_OMNI-C_HAP1_COR.fasta.gz) from the paper
 ## Summary High-quality genome assembly and annotation for *Dianthus
 carthusianorum* (haplotype 1), generated using PacBio HiFi reads and
 Omni-C scaffolding. Annotation was performed with BRAKER3 with short read
 RNAseq from leaf and flower bud tissues of the same individual (extracted
 from BAM file sent by Dovetail/Cantata) and short read RNAseq from\ young
 bud, intermediate bud, young flower, open flower, young leaf, and
 pollinated flower of an individual from Wallis as well as the
 ViridiPlantaea partition of OrthoDB v11 as evidence. More details can be
 found in the manuscript. The version here uploaded is the one used for all
 analyses and, which only differ in scaffold naming and orientation from
 ethDiCart_GR_1.1, which was submitted to NCBI (PRJNA1259412). ###
 Reference genome CARY_DIA_CAR_CH_CHANT_001_HiFi_OMNI-C_HAP1_COR.fasta.gz
 ### Structural annotation
 CARY_DIA_CAR_CH_CHANT_001_HiFi_OMNI-C_HAP1_COR.anno.gtf ### Functional
 annotation
 CARY_DIA_CAR_CH_CHANT_001_HiFi_OMNI-C_HAP1_COR.anno.emapper.annotations.xlsx ## Assembly Details * **File**: `CARY_DIA_CAR_CH_CHANT_001_HiFi_OMNI-C_HAP1_COR.fasta.gz` * **COMPOSITION** A = 157153546 (31.5%), C = 92322674 (18.5%), G = 92285134 (18.5%), T = 156903352 (31.5%), N = 6900 (0.0%), CpG = 30358188 (6.1%) * **SCAFFOLD** sum = 498671606, n = 62, mean = 8043090.41935484, largest = 39410985, smallest = 11396 * **SCAFFOLD** N50 = 33218876, L50 = 8 * **SCAFFOLD** N60 = 32392048, L60 = 9 * **SCAFFOLD** N70 = 31813274, L70 = 11 * **SCAFFOLD** N80 = 30730960, L80 = 12 * **SCAFFOLD** N90 = 30263282, L90 = 14 * **SCAFFOLD** N100 = 11396, L100 = 62 * **CONTIG** sum = 498664706, n = 131, mean = 3806600.80916031, largest = 25413205, smallest = 1324 * **CONTIG** N50 = 11463605, L50 = 15 * **CONTIG** N60 = 9809675, L60 = 20 * **CONTIG** N70 = 8828776, L70 = 26 * **CONTIG** N80 = 6382660, L80 = 32 * **CONTIG** N90 = 4014208, L90 = 42 * **CONTIG** N100 = 1324, L100 = 131 * **GAP** sum = 6900, n = 69, mean = 100, largest = 100, smallest = 100 All 15 chromosomes (n = 15) are represented. # Dianthus carthusianorum SNP panel and SNP sets from the paper *Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources* ## Summary This dataset contains a curated SNP panel and four SNP sets from ddRAD and WGS sequencing data in *Dianthus carthusianorum* and related taxa. Each dataset is tailored for a specific purpose: evolutionary lineage inference, seeding detection, phylogenetics, and genotyping error estimation. ### SNP.panel.vcf * **Purpose**: Serves as the reference panel for downstream SNP set generation * **Samples**: 136 individuals (42 ddRAD-SE, 63 ddRAD-PE, 31 ddRAD-WGS replicates) ### EvoLin_SNPs.vcf * **Purpose**: Assess evolutionary lineages, genetic structure and divergence within *D. carthusianorum* * **Samples**: 198 individuals (42 ddRAD-SE, 63 ddRAD-PE, 31 ddRAD-WGS, 62 WGS) ### Phylogenetic_SNPs.vcf * **Purpose**: Resolve broader phylogenetic relationships among *Dianthus* species * **Samples**: 37 individuals (including 5 related species + *D. carthusianorum* ESUs) ### Seeding_detection_SNPs.vcf * **Purpose**: Detect direct seeding and admixture in Swiss populations * **Samples**: 310 WGS individuals (10 per population) ### Genotyping_Error_ddRAD_WGS.vcf * **Purpose**: Assess error between ddRAD and WGS genotyping * **Samples**: 31 ddRAD-WGS replicated individuals