Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources

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 signi..., , # 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 (PR...,