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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 broadto 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