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Thu, 7 Feb 2008 13:49:55 -0500
- JBS-L - Josselyn Botanical Society discussion list of the University of Maine <[log in to unmask]>
- JBS-L - Josselyn Botanical Society discussion list of the University of Maine <[log in to unmask]>
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The response from Nolan Kane about botanical bar codes was very interesting.  

I was skeptical, too, so I asked my daughter for her input (and permission to share it).  Melanie is working on a PhD in plant systematics, studying Gomphandra, a genus of southeast Asian understory trees and shrubs.  I've heard a lot about her frustrations trying to isolate enough DNA to study from species with lots of other compounds that interfere.  She's in the Philippines again for three months of fieldwork but sent this response to my query.

--- quoted text from Melanie Schori ---
Botanical bar coding is a pipe dream, as far as I'm concerned.  Yes, it sounds 
very nice, but plants are not birds.  With birds, you can draw a bit of blood 
and get enough mitochondrial cells to do sequencing.  There are no nasty 
secondary compounds to get in the way.  There are also many fewer birds than 
there are plants.

The chloroplast gene matK has been sequenced in quite a few plants already, but 
sequencing DNA isn't something that can be done quickly by a handheld machine.  
The way it works now, you have an extraction procedure that lasts 1-3 or more 
hours, followed by PCR to amplify the DNA (at least 1 hour), and sequencing to 
read the genetic code (again, hours).  It involves a lot of very expensive lab 
equipment, not to mention very expensive enzyme for the PCR step.  The author's 
assurance that developing a handheld device to do all of this is just a matter 
of technology catching up is very blase and naive, in my opinion.  How would a 
little device break apart the cell walls, remove secondary compounds, isolate 
the chloroplast genome, add primers to find the right gene, and then sequence 
it (which requires fluorescently labeled base pairs) to have the results in 
about 1 minute?  It would be nice, but I don't see it happening in my lifetime, 
not without some major changes in how DNA is sequenced.

And as for everyone being able to become an expert on plants with a handheld 
scanner - who's going to identify and sequence all the plants in the 
Philippines and other tropical countries, including the ones that haven't been 
described yet?  How many herbaria would let their type specimens be sampled, 
especially for species known only from the type?  And how many people could 
actually afford such a device for incidental use?  Just imagine how it could be 
used by some people - you have a rare species on your property but you want to 
develop your land, so you use the scanner to find and eliminate every 

Oh, and then there's the small matter that some of the genes that are being 
targeted have been shown not to vary in some groups, like red algae.

People thought that the advent of molecular sequencing was going to solve all 
plant relationship and ID questions - it hasn't, and it won't.
--- end of quote ---