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bioRxiv · 10.64898/2026.02.11.705238

The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids

Wang, P.·Zuo, X.·Zou, L.·Wang, L.·Lin, L.·Wang, Z.·Zhang, Y.·Chen, X.·Meng, F.·Huang, H.·Lan, L.·Li, Z.·Wang, F.·Jin, Y.·Shan, H.·Zhang, R.·Kong, H.
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Abstract

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

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Wang, P., Zuo, X., Zou, L., Wang, L., Lin, L., Wang, Z., Zhang, Y., Chen, X., Meng, F., Huang, H., Lan, L., Li, Z., Wang, F., Jin, Y., Shan, H., Zhang, R., Kong, H.. 2026-02-12. The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids. https://doi.org/10.64898/2026.02.11.705238

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