Inter-haplotype inversions and repeat expansion in the sexually deceptive orchid Chiloglottis trapeziformis

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ID: 322697
2026
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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 Gb 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 (85.79-88.25% 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 inter-haplotype 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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Authors Zirui Zhang, Ashley Jones, Benjamin Schwessinger, Rod Peakall, Darren Wong
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Journal genome biology and evolution
Year 2026
DOI
10.1093/gbe/evag190
URL
https://doi.org/10.1093/gbe/evag190
Keywords Keywords not found

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