Sequencing orchid genomes: What are the benefits?

[BrassavolaStars]

Hello all,

I have recently become curious about genome sequencing for orchid genera. Since whole genome sequencing has gone down in cost from hundreds of millions of dollars to less than $1000 depending on circumstances, it has become more accessible.

What information could be gleaned from sequencing an orchid species? Would it eliminate the problem of NoIDs? Would it inform breeders on which genes pass down particular desirable traits?

I haven’t really studied this in any particular depth other than the occasional headline so I probably sound ignorant and like I don’t know what I’m talking about (because I don’t) .

I am particularly interested about the Zyopetalum genera as only about three or so species are actually used for hybridization in many cases.

Apparently only a handful of orchids have been fully sequenced.

[Orchid Whisperer]

Since there is no large (let alone comprehensive) database of genome sequencing data, it would probably not help the average grower with identification. Also, assuming you are not a geneticist, how would you interpret the sequencing data? I can't imagine spending the money to do sequencing of most of the NOIDS that I have had over the years.

I guess I am looking at it from a cost-benefit viewpoint, and from that perspective, would not be worth it to me. If you have financial resources to do the testing, there is nothing preventing you from following your curiosity.

[rymor]

Sequencing a whole genome provides a useful framework for comparative analysis with other sequenced genomes. Useful information such as gene and trait development and evolutionary relationships can be pulled from it.

It is still a bit costly and time consuming to use whole genomes for large-scale taxonomic/systematics studies with a lot of species, so biologists typically sequence individual genes or non-coding regions of the genome. Comparing these sequences can provide information on species identification and classification. This is what leads to plants being split/renamed.

In theory, you could compare the DNA sequences of an unknown plant and match it to previously sequenced DNA data available. To get a 100% ID, the plant of interest would have to been sequenced already.

[hypostatic]

I think I recently posted to a similar thread about this...

Anyway, there are actually a few complete orchid genomes that have been sequenced. All are publicly available:

Orchidaceae - Assembly - NCBI

[Herrania]

For most of what you want, whole genome sequencing isn't really the best way to go about it. Two far more common techniques are flash freezing tissue in a particular state (ie the buds opening) and seeing which genes are active. Or the gene for glowing will be attached to another gene, to make plants that should only glow in certain places or at certain times, as a test to see if the gene does what you think it does. This goes on long after getting the complete genome is done.

What a whole genome does help with, is quick comparisons after a gene is found. For instance, when the gene for how most birds create red and yellow pigments was found, it was a few keystrokes to find that the same gene exists in some of the more colorful turtles.

NoIDs could be handled without full sequencing, the big problem there is that ancestry studies often require HUGE databases of samples that can be tied to specific locations. Companies like 23andme used to provide huge discounts if you could prove that your ancestors all came from one remote area, just to get comparison samples.