The genome sequence of the orchid Phalaenopsis equestris

20 April 2015

​The cover of the first Nature genetics volume of 2015 shows a shining picture of the orchid phalaenopsis. The lab of Yves Van de Peer (VIB Department of Plant Systems Biology) can add an extra genome paper to its long list. Together with colleagues from Asia, they sequenced,  annotated, and dissected the Phalaenopsis genome. Without a doubt one of the most famous house plants after the Sanseveria.

Most plant genomes sequenced and published so far have been crop and model plants. Why would you want to sequence a house plant?
Yves: Orchids demonstrate astonishing evolutionary adaptations. Think for example of the flowers that sometimes mimic insects to attract pollinators. They are renowned for their diversity in specialized reproductive and ecological strategies. And that makes orchids extremely exciting to study on a genomic level. The new insights we gathered can also be used to start up new and more efficient breeding initiatives, for example using marker-assisted breeding.

Did the sequencing of Phalaenopsis present specific technical problems that had to be overcome?
We of course encountered the typical sequencing problems. Additionally, assembling the genome was not an easy task since Phalaenopsis is a heterozygote (ed. for every gene the plant holds several alternative sequences, referred to as alleles). With a heterozygous genome, the assembler might assemble the two alleles for one site separately, which would result in an excess of the assembly with half of the average sequencing depth. Since Phalaenopsis is the first plant of its kind
now being sequenced, we had no available genomes of close relatives to fall back on, which complicated the gene prediction procedure significantly.

Can you summarize the most exciting findings?
Phalaenopsis equestris has a moderately large genome of 1 Gb with approximately 30,000 predicted genes, which is a fairly typical number for an angiosperm. Interestingly, the intron length is greater than expected. For example, the maize genome is twice as large as that of P. equestris, but the total intron length in maize is only half that of the orchid. A bit paradoxically we found that the total number of flower genes was lower than, for example, rice. However, this feature does not affect morphology per se and the morphological novelties of orchids most likely originate from unique regulatory interaction networks. Finally, for the first time, this paper provides insights into the genome of a plant that relies on CAM photosynthesis CAM metabolism is characterized by a more efficient carbon fixation when water is limited. Orchids do indeed originate in the tropics, but many of them are epiphytes: they live on other plants and often lack a root system, which limits water availability over time.

Cai, et al.
Nature Genetics, 2015

© Nature Genetics, 2015