T2T-CHM13v2.0 gene-feature GFF3 (chr-named) with the pseudoautosomal P2RY8 chrX locus restored

This dataset is a lightweight gene annotation of the T2T-CHM13v2.0 human genome assembly (NCBI GCF_009914755.1), intended as the annotation input for Oxford Nanopore adaptive-sampling target/BED design (e.g. the ont-bed-generator tool). It is derived from the official NCBI RefSeq annotation release RS_2025_08 by two lossless transformations and one documented addition: Gene features only — only records whose GFF3 type (column 3) is gene are retained, reducing the ~78 MB full annotation to ~2 MB (41,562 gene records). Chromosome renaming — sequence identifiers are renamed from RefSeq accessions (e.g. NC_060925.1) to UCSC-style names (chr1 … chrX, chrY), using the name↔accession table from the assembly's official assembly_report.txt. PAR1 P2RY8 restoration — the chrX pseudoautosomal copy of P2RY8 is added. P2RY8 is a PAR1 gene and is therefore present on both sex chromosomes, but the RS_2025_08 build annotates it only on chrY (whereas its PAR1 neighbour CRLF2 is annotated on both). The added record uses the coordinates of the NCBI curated transcript NM_178129.5 aligned to chrX of hs1 (chrX:1304499–1338509) and the same Entrez identifier (GeneID:286530) as the chrY copy; its GFF3 source field (NCBI_RefSeq_curated_NM_178129.5_PAR1) records this provenance in-file. The production chain is fully scripted and reproducible (build_gene_gff.sh, available in the ont-bed-generator repository); no coordinate is hand-authored. The asset is tied to NCBI RefSeq release RS_2025_08 and should be regenerated when a newer annotation release is published — ideally once the upstream chrX P2RY8 omission is corrected, at which point step 3 becomes unnecessary. Scope note. Pseudoautosomal-gene annotation is known to be inconsistent across providers (NCBI, UCSC and Ensembl each differ and are individually incomplete for PAR1). This dataset keeps the traceable NCBI annotation as its base and restores only the single, biologically required, NCBI-sourced chrX P2RY8 locus, rather than switching to a source with different PAR gaps.