Download DNA Barcoding

Introduction to
DNA Barcoding
Biotechnology II
Essential Question(s)
 What
is DNA Barcoding?
 How are species identified using DNA
barcodes?
Classification of Organisms
 Taxonomy-
discipline
used to name living
organisms

Placed in specific
groups based on
 Comparative
anatomy
 DNA
 Chemical makeup
 Geographic location
Binomial Nomenclature
 First
instituted by Carolus
Linneus in 18th century
 Two-part Latin name given
each organism


First part – genus
Second part - species
 First
letter of genus is capitalized, the
entire binomial is italicized
or underlined

Ex. Panthera pardus - leopard
Hierarchical ClassificationLinnaean System
 Linneus
further
grouped organisms
into increasingly
inclusive categories

From very
broadto specific
Identifying Organisms

Grown in importance in
recent years because of




global climate change
habitat destruction
Trying to preserve biological
diversity
Biological diversity
important

Maintaining ecological
communities



more stable- more
available resources
More resistant to
environmental stresses
More resistant to invasion
by non-native species
Identification of plants,
animals, and microbes
 Know
very little about
species diversity



Fewer than 2 million of
estimated 5 to 50 million
plant and species have
been identified
Rate of extinction has
increased from about 1
species per million to 1001000 species per million
Most of these species have
yet to be identified
Classical taxonomy

Inadequate for
cataloging the
biological diversity
before it disappears


Specimens must be
carefully collected and
handled to preserve
distinguishing
characteristics
Differentiating subtle
anatomical features
requires highly trained
specialists
DNA technology


Advancements allow
even non-experts to
identify species
objectively
Accomplished through
DNA Barcodes

Barcodes are unique
pattern of DNA
sequence that
identifies each living
thing

Usually around 700
nucleotides in length
International Barcode of Life
 Organization
that have collaborators in
over 150 countries that are participating
in collecting samples to identify plants
and animals worldwide
 Global Biodiversity Challenge
Why DNA Barcode?

Help with conservation effort


Identify and stop illegal trading


Ex. Ivory trade
Make consumers safe



Identify species associated with specific
habitats
Ex. Foods properly labeled
Students from Trinity High School in New York city
found that 25% of 60 seafood items sold in
grocery stores were mislabeled as more
expensive species
Identify life stages of animals, previously hard
to identify
DNA Barcodes
 Relies
on short, highly variable regions of
DNA that can be amplified by Polymerase
Chain Reaction (PCR) and later
sequenced for species identification
 Bar codes used depend on organism



Plants – region of chloroplast gene that
codes for large subunit of RuBP Carboxylase
Animals –region of mitochondrial gene that
codes for cytochrome c oxidase
Bacteria – region of gene that encodes for
16S rRNA
Why Cytochrome c Oxidase
subunit 1 (COI) for Animals
The Ideal Gene to Study is…
 Present
in all species.
 Variable,
variable.
The COI Gene…

but not too
among
scientists around the
world.

 Standardized

All eukaryotes contain
mitochondria; COI
encodes a mitochondrial
protein needed for cells to
make ATP.
COI is almost identical
within a species but varies
between different species.
Agreement among
scientists that the COI gene
is used for animal
barcoding.
Steps in DNA Barcoding






Collect Specimen
Record where specimen
collected
Isolate DNA
Amplify DNA by
polymerase chain
reaction
Sequence amplified
DNA
Search DNA databases
for matches
Basic Local Alignment Search Tool BLAST

Can be used to:




Compare 2 or more DNA
sequences to each other.
Compare 2 or more protein
sequences to each other.
Compare a single sequence
to many sequences found in
databases.
You will perform a
nucleotide BLAST (blastn)
search to find the best
possible match for your
unknown sequence.
Novel DNA Barcodes
 Can
be submitted to the database at the
Barcode of Life Data System (BOLD)
 http://www.boldsystems.org at the
University of Guelph
Class Activity
 Complete
an activity to familiarize
yourself with BLAST and BOLD