PanMD: An Apple (Malus domestica) graph pangenome dataset

This dataset contains a reference-anchored *Malus* graph pangenome built from35 assembly or haplotype paths. The graph was constructed withMinigraph-Cactus through the `cactus-pangenome` workflow, using`MdCameo_A` as the reference. | Item | Value ||---|---:|| Input assembly/haplotype paths | 35 || Reference path | `MdCameo_A` || Reference chromosomes | 17 (`1A`-`17A`) || Reference span | 653,882,183 bp || Non-reference VCF samples | 34 || Records in `pandomestica.vcf.gz` | 13,400,633 || Records in `pandomestica.raw.vcf.gz` | 21,336,732 || Graph nodes across 17 clipped chromosome graphs | 81,943,509 || Graph edges across 17 clipped chromosome graphs | 111,374,667 || Total graph sequence length across those graphs | 1,588,506,182 bp || Construction software | Cactus 3.0.0 || Cactus commit | `4838a924e8f9588ccafd90a2f67e2b991b4e5995` || Workflow engine | Toil `9.1.0-e341bb669efe78f93308e5ff1f02f7e375973511` || Workflow completion date | 2025-11-20 | The graph statistics are sums of the chromosome-level values stored in`pandomestica.stats.tgz`. ## Included genome paths The Cactus input sequence file contains 35 biological assembly/haplotypepaths. `MdCameo_A` is the reference and is therefore not repeated as a samplecolumn in the VCF files. The VCFs contain the other 34 paths. Each label is represented as an independent path/sample. Paired labels such as`_A`/`_B` or `_1`/`_2` have not been merged into a single diploid VCF sample. | Accession or label group | Included path labels ||---|---|| Antonovka | `MdAntonovka_A`, `MdAntonovka_B` || Cameo | `MdCameo_A` **(reference)**, `MdCameo_B` || COP | `MdCOP` || Fuji | `MdFuji_1`, `MdFuji_2` || GDT2T | `MdGDT2T_1`, `MdGDT2T_2` || Gala | `MdGala_1`, `MdGala_2` || Granny | `MdGranny` || HF | `MdHF` || Honeycrisp | `MdHoneycrisp_A`, `MdHoneycrisp_B` || jiguan | `Mdjiguan` || M9 | `MdM9_1`, `MdM9_2` || MM106 | `MdMM106_1`, `MdMM106_2` || OregonSpur | `MdOregonSpur` || Orin | `MdOrin` || Qincui | `MdQincui_A`, `MdQincui_B` || Qinguan | `MdQinguan_A`, `MdQinguan_B` || Ralls | `MdRalls` || RoyalGala | `MdRoyalGala` || SD | `MdSD` || WA38 | `MdWA38_A`, `MdWA38_B` || Msieve | `Msieve_1`, `Msieve_2` || Msylve | `Msylve_1`, `Msylve_2` |