DNA sequencing

Fernando Rivadavia Lopes (ferndriv@usp.br)
Sun, 1 Oct 1995 03:11:45 -0500 (CDT)


> From speaking with Steven Williams, it seems to me that this is really
> only good when comparing species that are closely related. He had men-
> tioned that, from what his testing showed, Nepenthes are related to rhu-
> barb.
> Well as luck would have, the year I spoke with Dr. Williams my twenty-
> something year old rhubarb flowered for the first time. The inflore
> scence was similar, to my untrained eyes, to a male Nepenthes inflore
> scence. The seed pods, however, looked like those of begonias, having
> three compartments. I've not seen a Nepenthes seed pod in person and
> so I don't know if they are alike. But could they be related? Or do
> you start to get inconclusive/misleading data when comparing very dis-
> similar plants' DNA?

Phylogeny through DNA sequencing can be used both for distantly
and for closely related organisms, it all depends on what you want and
what DNA sequence you decide to use. There are certain genes which are
extremely well preserved in their sequences of the bases G, C, T, and A.
These genes are vitally important because of the proteins they code for.
There is the extreme case of the ssu-rDNA gene which is present in ALL
organisms, from bacteria to humans to slugs to mushrooms to watermelons.
This gene is composed of various segments. Some of these
segments (called exons) code for a protein, while other segments (called
introns) are at one moment excised and their sequences don't code for the
protein. The base sequence of the exons in this gene are so highly
preserved (because of the importance of the protein they code for) that
it can be used to compare any and all organisms to get information
about relationships at high taxonomic levels. There are phylogenetic
trees built from this information showing the relationship between the
various taxonomic groups, like which stemmed from which at how many
million years ago.
The sequence of the introns can be used to do the same with
closely related organism. Mutations in the introns are more likely to not
cause damage to the protein coded by that gene, and thus accumulate more
rapidly than in the exons. If you try to use the intron sequence to
compare distant organisms, it probably won't work since too many mutations
are likely to have already occured from the time the organisms separated
on the evolutionary scale.
I believe DNA sequencing will be a must for taxonomy in the
future. The amount of information obtainable is fantastic and it's
mathematical. You can quantify the relationship between the organisms,
something traditional taxonomy points out, but doesn't guarantee. Not
that DNA sequences alone are enough, but are sure a VERY strong
indication. Much better than leaf shape, flower color, etc., in my
There is a very interesting article on CP phylogeny in Science
257, dating 11 September 1992, by Victor Albert, Stephen Williams, and
Mark Chase. They sequenced a specific gene (called rbc-L, present in all
plants) from a few plants in almost all CP genera and put these sequences
together with those from various other higher plant groups. One of the
interesting result was that Roridula is sister to Darlingtonia,
Sarracenia, and Heliamphora. Another is that Byblis is close to
Pinguicula and Utricularia and VERY far from Cephalotus, with which it is
often placed. The Drosera called my attention the most. First of all,
they really are close to Nepenthes. Second, Drosophyllum stems off from
Drosera before Dionaea and the first Drosera to stem off is D.regia. The
Drosera then split into 2 groups. In one of these D.burmanni stems to one
side while D.capensis and D.filiformis stem to the other. In the other
group, D.binata and D.peltata stem to one side while D.petiolaris and
D.dichrosepala stem to the other.
I only discovered this article a few weeks ago and recommend it
to all of you. It might be a bit too complicated for non biologists, but
still worth looking into. Happily, this info about the Drosera supports
one of my highly speculative hypothesis, mentioned during a discussion on
Drosera evolution with Jan Schlauer on this listserv a few months ago.
I'd mentioned that a thick-rooted species like D.binata probably
originated the tuberous Drosera while D.petiolaris and the pygmies must
be closely related groups, due to certain morphological similarities
(like small lamina and long, narrow petioles, present in most species).