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Orchid Genome Is Sequenced

As one of the most diverse plant families, the orchid now has had its first whole genome sequenced and the result will ultimately appear as a cover story in Nature Genetics and was published, in advance, online, on November 24, 2014, in an open-access article in Nature Genetics. This study was an international collaboration, including the 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 (image), which is an important parental species for breeding of commercial phalaenopsis strains. P. equestris is also the first plant sequenced that has 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 seen in any sequenced plant genomes. Further analysis indicated that transposable elements in introns are the major reason for the large size of introns in the orchid genome. The orchid genome contains a high degree of heterozygosity, thus posing a 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 the orchid. It was also reported that the evidence was found 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 analyzing 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, and the genome breeding and improvement of orchid varieties, to further enhance the efficiency of orchid breeding and facilitate orchid horticulture research.

[Press release] [Nature Genetics article]