Gapless genome sequences reveal the hybrid origins of Hong Kong’s iconic orchid tree

April 25th is an international DNA day, marking the completion of a decade-long project ordering the DNA of the Hong Kong orchid tree Bauhinia x Blake Anadan, the floral emblem of Hong Kong.

Published in Gigascience and led by scientists at Hong Kong China University (CUHK), the study presents a complete, gapless sequence of the Bauhinia genome from one end of the chromosome to the other end (telomere to telomere or T2T).

This beautifully ornamental Bauhinia species, featured in Hong Kong’s flag and currency, is touted for its impressive purple orchid-like flowers, but can be traced back to the accidental discovery by French horticulturalist Jean Marie Delavai on Hong Kong Island in the 1880s.

Later, it was judged to be completely barren and could only grow by propagating from cuttings, making this impressive species a scientific mystery.

Morphological and single genes and marker studies suggest that this species may be a hybrid between Bauhinia purple and the varieties, but to date there remains a lack of conclusive confirmation, particularly at the genomic level.

The historical and cultural interests of Bauhinia in Hong Kong led to the community-crowded genomic projects, attempting to answer some of the questions about the origins of species, and launched the Bauhinia genome project in 2015, raising enough money to arrange the transcriptomes of three important species.

The team began moving on to the full genome in 2019 by combining cutting-edge second and third generation sequencing technologies. This multiplatform approach enabled the first chromosomal scale draft assembly of hybrids and their putative parent species.

With the advent of the first human T2T genome in 2023, computational biologists at the National University of Singapore used new algorithms to refine assembly and achieve the haplotype-degrading genome of T2T. The final genomic assembly reveals 28 complete chromosomes (14 inherited from each parent) and is formed through genetic chimera that drives peculiar hybridization events, their vivid floral and ecological adaptability.

This new T2T level assembly completes sequencing efforts, allowing for accurate tracking and analysis of genetic variation in parent lines and their hybrid offspring, and promotes a comprehensive understanding of the underlying genetic mechanisms of its abnormal flowering and reproductive properties.

This project clearly resolves the parent-child relationship problem in Bauhinia in Hong Kong, B. bariegata is a paternal parent, B. Purpurea has been identified as a motherly parent. It creates a hybrid despite the two species being separated for 13.4 million years.

Transcriptome profiling of flower tissue (a method of tracking gene activity) highlighted the similarity of B. blakeana to maternal parents, revealing distinct expression patterns among the three species, particularly in biosynthetic and metabolic processes.

New transcriptome data also shed light on the heterosis or hybrid vitality process. This is a phenomenon in which hybrid descendants display extended or superior properties compared to their parents.

“When we launched this grassroots community project and educated the public about the potential for rapid development of genomics, it rarely became a complete genome with no gaps covering the 29,000.7 million base pairs,” said Scott Edmunds, co-founder of the community-led Bauhinia Genome Project.

“When we proposed the project due to the accuracy and cost of technology at the time, full T2T genomics was impossible. I am very pleased to be able to say “to carry out the mission” in the genome of Bauhinia, starting as a generally attractive civic science project by conducting outreach and discussions on Hong Kong schools, radio and television. ”

Through this haplotype degradation and production of gapless T2T genomes, researchers have advanced their understanding of the fascinating floral colour traits and the genomic structure and genetic mechanisms underlying the expanded flowering period of this common and enigmatic ornamental tree, which serves as a case study to investigate the properties of other hybrid species.

The stress-resistance-related genes, flower-shaped trait regulatory genes, and medicinal component-related genes identified in this study provide many new molecular targets for future applications, including improvements in plant stress resistance, optimization of decorative traits, and advances in biosynthesis of pharmacologically active compounds.

Stephen Tsui, a Hong Kong citizen and researcher at Hong Kong China University, said, “The hybrid genome presents important assembly challenges due to its high heterozygosity and structural complexity. Data – a noticeable improvement over traditional workflows.

“By decoding these haplotypes, we not only solved the old mysteries of their origins, but also revealed how parental allelic interactions form the iconic floral features of hybrids.

“Our research also serves as a model for exploring the properties of hybrid species using the T2T haplotype degradation genome, providing a novel approach to understanding the genetic interactions and evolutionary mechanisms of complex genomes.

As an open science project, all resources generated in this study are freely available for future genetic research, breeding programs, and conservation initiatives for Bauhinia species. The materials and protocols can also be used for wider educational reuse in Hong Kong and beyond.