annotation_hla.gff

We re-scaffolded the Hipposideros larvatus genome to the chromosome level by anchoring Hi-C paired-end reads to the draft assembly using Juicer v1.6. This process yielded a final assembly comprising 15 autosomes and one X chromosome, which is consistent with the published karyotype (2n = 32). For gene annotation, a homology-based pipeline was employed: GEMOMA v1.9.0 was applied to the repeat-masked assembly, with guidance from protein sequences derived from ten phylogenetically representative species.