DNA Barcoding and Genomics at L.A.B
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DNA Barcoding and Genomics at L.A.B

I’m Amy Driskell and I’m on the staff of the
Laboratories of Analytical Biology or L.A.B. here at Natural History. We’re on the first floor of the West Wing and
we have labs as well out at MSC in Suitland so you may not know of us, but I’m going to tell
you today about some of the work that I’ve been doing there for the last eight years. In 2005 L.A.B. was awarded a reasonably sized
pot of money to begin a DNA barcoding program. And I arrived in December of 2005 as the project
manager for this program. And my job since then has been to establish collaborations, plan,
and manage DNA barcoding projects. So what is DNA barcoding and
why are people willing to fund it? Well, essentially a DNA barcode
is a fingerprint for a species, basically it’s a sequence that can be taken
from anything and be compared to a database and act as an identifier. This is not new science, it’s been going on a
long time, but barcoding was an international collaboration where we had agreed-upon
standards and requirements for sequences to be labeled as DNA barcodes. And the idea was we would take the gene,
so in animals the gene is the CO1 gene of the mitochondrial genome and in plants it’s a couple
of chloroplast genes. We would sequence this gene from as many animals as we could and fill
up a database. And these would be high quality sequences. And then these databases, these
public databases of barcode sequences could be used for identification of unknown sequences. So in a perfect world you could have a soup
of unknown composition, you could extract its DNA, you really could, and sequence it, and then compare it to the databases of
barcode sequences and determine its components. So that’s in a perfect world. And of course the world is imperfect, and this
barcode gene that was chosen for animals, the CO1 gene, is not easily sequenced from
many large groups of animals such as nematodes. That’s a lot of biodiversity. And it’s difficult to
sequence out of many different kinds of other organisms such as animals that eat other animals.
So in terms of universality it’s not really that universal. In addition the databases are really not, are sparsely
populated in terms of biodiversity. If you have an unknown bird sequence then you might find a match in
the database, but if you have an unknown rotifer sequence, there’s no chance. So being part of the museum community we
decided it was our job to fill up these reference databases with as many barcodes for the
organisms in the tree of life as possible. So these are the organisms, specimens that have
passed through our hands in the last eight years, these are just numbers of specimens, not barcodes.
You can see we have about 90,000 specimens here. Here are the success rates for
sequencing the easily sequenced groups, when you have good specimens. It’s actually even higher in many of those cases. I can’t say that we’ve barcoded successfully every
single specimen on this list because as I said, many of the groups are difficult to impossible to barcode,
although we have tried our best. We haven’t given up yet. But in the process of doing this we have
created a very large DNA library of high-quality DNAs that will be permanently stored here
and available for future research, so … the program has done that. We’ve had a number of different kinds of DNA
barcoding projects at the L.A.B. and I’m going to tell you about two that sort of show
you the different ends of the process. The first one has been in collaboration
with the Bocas del Toro Research Station of STRI in Panama. Every year we have gone down for
their taxonomy training workshops and as the taxonomic experts collect and name
the specimens we have harvested tissues for DNAs. So in this way we have had a pretty fruitful
collaboration. We’ve got a pretty good biodiversity sample and lots of good DNAs from
freshly killed or still kicking animals. And we hope that this alliance can continue
in the future because we don’t have any worms, for example, annelids. Another project is sort of tool-building and
this has been funded by the FDA. We are developing a method to identify fish fillets
with DNA barcodes. And while it’s very easy to sequence fish, very easy to barcode
fish, what’s missing is a complete reference library of fish sequences. So the FDA has funded field trips to the Philippines
for the last four years, actually field trips to the Philippines fish markets. Undertaken by Jeff Williams
in the Division of Fishes and his collaborators. And in the first three trips they sampled only 1200 specimens
from which they got more than 780 species. So the fish markets of the Philippines are remarkably diverse. Now DNA barcoding as part of my program
has sort of been declining in years as a major focus and we have been picking up more and
ramping up more to the genomics thing in order to satisfy the needs of many
of the curators here at the museum. And you might have heard the word genomics
or something else “omics.” And exactly what does that mean? And I think it means, in general,
we use that word when we are sequencing more of the genome than just one gene.
Not just the barcode gene but thousands of genes at one time. And there’s a newer sequencing technology
which we call nextgen sequencing, next generation sequencing, which makes it
possible to get millions of reads in one run compared to the maximum 96 reads
on our more traditional machines. So, in last year Life Technologies
gave us a 1.5 million dollar gift and included three Personal Genome
Machines which are nextgen sequencers. And although it will only sequence
your whole personal genome if you are a prokaryote, it still produces 3 to 6
million reads at one time. And this is more than enough data to do mitochondrial,
sequence entire mitochondrial genomes or chloroplast genomes, which we’ve done
a number of. We have other projects too including identification tool development
and searching for low cipher phylogenetics. So that’s the story of the L.A.B.
We’re on the first floor, West Wing, we have a lot of equipment, we can do
a lot of things, and a lot of people work there. Thanks.
[laughter] [applause] Why are nematodes so difficult? Because they are the coolest critters. [laughter] Oh, why are nematodes
so difficult to sequence? Well, it’s not exactly clear. They’re very old,
they’re very divergent and so it’s not clear whether they rearrange their genomes like
say snails do but we know that they have a very funny base composition because
we’ve done a couple of mitochondrial genomes, and it’s just that the primers that work on
other animals for sequencing, just don’t.

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