dna barcoding in animals
TRANSCRIPT
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DNA BarcodingIn Animals
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CONTENTS
• HISTORY• INTRODUCTION
• BARCODE OF LIFE COMMUNITY
• HOW BARCODING IS DONE
• WHY BARCODING IS DONE
• APPLICATIONS
• DNA BARCODING IN PAKISTAN
• BARCODE DATA ANALYSIS
• CONCLUSION
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I. Taxonomic Identification• Morphological characters• Breeding• Biology• Host plants etc.
II. Molecular Identification RNA/DNA nucleotide data Protein analysis
Biological Unit Identification
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Molecular Identification
Use of DNA/RNA and proteins sequence data for individual or species identification by
• Sequence comparisons • Constructing phylogenetic trees• Other available tools
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Why Molecular Identification?
• Clear genetic basis• Deformed/broken samples are OK• DNA from fossilized specimens can be used• Identification of immature stages, or concealed
stages possible• Quick and unbiased• Reliable
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Deoxyribonucleic Acid
• DNA is:
• The hereditary material in humans and almost all other organisms.
• Same in nearly every cell of body• Mostly located in the cell nucleus
(nuclear DNA)• Also found in small amount in the
mitochondria (mitochondrial DNA).
ghr.nlm.nih.gov
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Barcodes:• Uniform Product Code• Consists of hidden language
made up of series vertical bars lines of varying width
• Used in identification by optical or laser scanner
The system of showing information in the form of barcodes
Barcoding
en.wikipedia.org/wiki/Barcode
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DNA Barcoding• DNA barcoding is a standardized approach to identifying
plants and animals by minimal sequences of DNA, called DNA barcodes.
• A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species.
www.barcodeoflife.org/content/about/what-dna-barcoding
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Marker
• The standard region used to generate DNA barcode
• Different in different species
• In animals it is COI or cox1 (cytochrome C oxidase 1) present in mitochondrial gene
www.dnabarcodes.org
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An Internal ID System The Mitochondrial Genome
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The Chosen Gene
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Why COI Gene?
• Standard region • Lack insertions or deletions• Ease of isolation• Greater differences among
species• High copy number (100-10,000 )• Relatively few differences within
species• Absence of introns• Range of mutational rates in
different regions of the molecule
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Standard Barcode region for Prokaryote
• SSU • lSU
Nuclear DNA - rRNA• Easily available• High copy number• High degree of
variation• Find and Amplify
• Inter Transcribed spacer
• Ribosomal genes code for rRNA• Spacer regions are transcribed but then removed• Region has restriction site polymorphism between
species
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Using DNA Barcodes
• Establish reference library of barcodes from identified voucher specimens
• If necessary, revise species limits• Then:
• Identify unknowns by searching against reference sequences
• Look for matches (mismatches) against ‘library on a chip’• Before long: Analyze relative abundance in multi-species
samples
www.springer.com/us/book/9781617795909
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History Of DNA Barcoding
• Carl Woese gave this concept first time.
• He used rRNA and molecular markers like rDNA and mtDNA to discover Archea i.e. prokaryotes and then for drawing evolutionary tree.
• In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Paul Hebert
www.barcodeoflife.org/content/about/what-dna-barcoding
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Our Planet: Home to approximately 10-100 million species
Our Brain:Able to recall and recognize perhaps 1000 species
Why DNA Barcoding?
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Ten Reasons For Identifying Species By DNA Barcodes
1. Works with fragments2. Works for all stages of life3. Unmasks look-alikes4. Reduces ambiguity5. Makes expertise go further6. Democratizes access7. Opens the way for an electronic handheld field guide, the Life
Barcode8. Sprouts new leaves on the tree of life9. Demonstrates value of collections10. Speeds writing the encyclopaedia of life
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• Promote barcoding as
a global standard• Build participation• Working Groups• BARCODE standard• International Conferences• Increase production of public BARCODE records
Networks, Projects, Organizations
Barcode of Life Community
http://www.barcodeoflife.org/content/about/barcoding-landscape
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There are four components of
barcoding projects:
1. The Specimen Collection
2. The Laboratory Analysis
3. The Data Base
4. The Data Analysis
Components Of Barcoding Projects
http://www.barcodeoflife.org/content/about/what-dna-barcoding
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Method
http://www.barcodeoflife.org/content/about/what-dna-barcoding
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DNA Barcoding Lab Scenes
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Barcode Analysis
• Nucleotide identities/matches
• Distance analysis• Barcoding gap• Cluster analysis
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Methods
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Applications Of DNA Barcoding
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Identification Of All Life Stages
www.springer.com/us/book/9781617795909
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Identification Of Fragments Or Products Of Organisms
• Illegally traded bushmeat, sharkfins, skins
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?
Food Safety and Accuracy
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For Example
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Disease Vectors
Culex pipiensWEST NILE VIRUS
Culicens incidensNON-VECTOR
Egg raft
?
?
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Dengue transmission cycle West Nile Virus transmission cycle
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Differentiating Cryptic Species
• Astraptes fulgerator, skipper butterfly.
• Wide-ranging; southern U.S. to northern Argentina.
• In northwestern Costa Rica, comprises complex of 10 sympatric species that are distinct in DNA sequence (COI), larval coloration, food plants, and subtle morphological traits.
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Sympatric larvae of Astraptes fulgerator
Food plant: Celtis iguanaea
Food plant: Trigonia (2 species); larvae will starve if reared on plants used by other larval types.
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Sisterspecies vs congeners
Panthera leo (lejon)
Panthera tigris (tiger)Motacilla flava (gulärla) Motacilla alba (sädesärla)Carabus nitens (guldlöpare) Carabus coriaceus (läderlöpare)
Sisterspecies vs congeners
Sylvia minula (ökenärtsångare)
Sylvia curucca (ärtsångare)
Sisterspecies vs congeners
Pipistrellus pipistrellus (Pipistrell)
Pipistrellus pygmaeus (dvärgfladdermus)
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Identification of stomach contents, trace ecological food-chains
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Other Applications
• Customs control• Invasive species control• Police • Agriculture• Forestry• Conservation• Education • Estimating species diversity• Resolving commercial disputes• Etc
www.springer.com/us/book/9781617795909 www.ijergs.org
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iBOL nodes
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Canadian Centre for DNA Barcoding
NIBGE
Funded by:
HEC ; iBOL
Pakistan Form Barcode Focal Point
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Barcoding Species From Pakistan
http://ibol.org/pakistan-to-form-barcode-focal-point/
• About 2,000 arthropod species have been barcoded under the NIBGE-BIO collaborative project "sequencing DNA barcodes of economically important insect species of Pakistan.“
• DNA barcoding is also being done on spiders, fishes and mosquitos by different universities and researchers to identify their species.
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http://www.dawn.com/news/1203605
Illegal Wildlife Trade
• Pakistan is using DNA barcoding to check illegal wild life trade.
CASE STUDIES:
• Last year, over 200 black pond turtles destined for Bangkok, were confiscated at the Karachi airport.
• Another consignment of turtles of the same species was caught at the Chinese border which was then repatriated to Pakistan.
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• The DNA testing method was first tried in March 2015 when customs officials confiscated a shipment of nearly 2,000 kilograms of freshwater turtle meat worth $60 million.
• The confiscated consignment was of turtles native to the Indus River and listed in the (CITES), that restricts trade to ensure its survival.
• As many as 4,000 turtles were killed and were being shipped out of Pakistan.
Continued…
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Strength• Offers alternative taxonomic identification tool for situations
in which morphology is inconclusive. • DNA barcoding can speed up identification of new species • Potential capacity for high throughput and processing large
numbers of samples• Identify specimens – a global identification system• Discover new species – aid and speed up the discovery of the
remaining biodiversityFocus on one or a small number of genes provides greater efficiency of effort.
• Cost of DNA sequencing is dropping rapidly due to technical advances.
• Once reference database is established, can be applied by non-specialist.
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Thank you!