Scientists Completed Whole Genome Sequencing of a Butterfly Orchid

Shenzhen, China — As one of the most diverse plant family, orchid now has its first whole genome sequenced and the result will appear as a cover story in Nature Genetics and was published in advance online at

This study was an international collaboration, including National Orchid Conservation Center of China (NOCCC), BGI-Shenzhen, Tsinghua University, Ghent University, Chengkong University and Institute of Botany Chinese Academy of Sciences.

The research team carried out the whole genome sequencing of Phalaenopsis equestris, which is an important parental species for breeding of commercial phalaenopsis strains. P. equestris is also the first plant sequenced with crassulacean acid metabolism (CAM). The assembled genome contains 29,431 predicted protein-coding genes. The average intron length is 2,922 base pairs, which is much longer than any sequenced plant genomes. Further analysis indicated that transposable elements in intron are the major reason for the big size of introns in the orchid genome.

Orchid genome contains high degree of heterozygosity, thus post great challenge for the whole genome sequencing and assembly. In this study, researchers found that due to heterozygosity, the derived contigs were likely to be under-assembled and may be enriched for genes involved in self-incompatibility pathways. Those genes could be candidates for further research on the mechanism of self-incompatibility in orchid.

It was also reported the evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, which explained why orchid developed into one of the largest plant families on earth.

Comparative analysis was conducted on homolog genes between orchid and other plants, such as Oryza sativa, Sorghum bicolor and Zea mays. After analyzed six key enzymes in CAM genes, authors identified the gene duplication and loss in CAM genes along the lineage to orchid. This result suggests that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris.

Finally, the team found expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

Orchid has become a highly endangered species because of illegal collection and habitat loss. The complete genome sequence of P. equestris will provide an important resource to explore orchid diversity and evolution at the genome level. The genome sequence will also be a cornerstone for the development of new concepts and techniques in genetic engineering, such as molecular marker, the genome breeding and improvement of orchid varieties, to further enhance the efficiency of orchid breeding and facilitate orchid horticulture research.

About BGI

BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications. BGI has achieved a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 600 publications in top-tier scientific journals. BGI Tech Solutions Company, a subsidiary of BGI, provides sequencing and bioinformatics service solutions for global biomedical, agricultural, and environmental customers.

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