ArticleGenome biology and evolution2026
Interhaplotype Inversions and Repeat Expansion in the Sexually Deceptive Orchid Chiloglottis trapeziformis.
Article in Genome biology and evolution, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
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.
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