Interhaplotype Inversions and Repeat Expansion in the Sexually Deceptive Orchid Chiloglottis trapeziformis

High-quality nuclear genome resources remain scarce for most orchids, particularly Australia's diverse terrestrial lineages. Chiloglottis trapeziformis is a well-studied sexually deceptive orchid that provides a valuable system for investigating orchid genome evolution, structural variation, and the molecular basis of specialized pollination. Here, we integrated PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C chromatin-contact data to generate the first chromosome-scale, haplotype-resolved nuclear genome assembly for any Australian terrestrial orchid. Hi-C guided scaffolding resolved two haplotypes into 20 chromosomes each, consistent with the reported karyotype and genome size (2n = 40, haplotype sizes of 1.58 and 1.91 Gb). Genome completeness was high for both haplotypes, recovering 94.67% and 94.82% single-copy BUSCO genes for Haplotype 1 and Haplotype 2, respectively. De novo repeat annotation revealed a repeat-rich genome (85.79% to 88.25% repetitive sequence), dominated by LTR retrotransposons. Evidence-guided annotation identified 16,287 and 16,548 protein-coding genes in Haplotype 1 and Haplotype 2, respectively. Phylogenetically informed comparisons placed C. trapeziformis as sister to Anoectochilus roxburghii among sampled Orchidoideae and showed broad gene-order conservation. Comparing the two haplotypes for structural variation, we identified large interhaplotype inversions containing functionally annotated genes with detectable RNA expression, with focal examples further supported by local Hi-C contact patterns and breakpoint-level inspection. Inversion-overlapping genes did not show elevated dS relative to collinear background. This assembly and annotation resource provides a foundation for population and conservation genomics, structural and comparative analyses, and genome-enabled hypothesis testing of molecular traits underlying sexual deception in orchids.