dna sequencing technology and its applications in evolution research
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DNA Sequencing Technology and its Applications in Evolution Research. Julie Urban, Ph.D. Assistant Director, Genomics & Microbiology Laboratory NC Museum of Natural Sciences. Planthopper Evolution. 1953. Planthopper Evolution. 15 Feb, 2001. Planthopper Evolution. (2001). X. X. - PowerPoint PPT PresentationTRANSCRIPT
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DNA Sequencing Technology and its Applications in Evolution Research
Julie Urban, Ph.D.Assistant Director, Genomics & Microbiology Laboratory
NC Museum of Natural Sciences
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Planthopper Evolution
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Planthopper Evolution1953
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15 Feb, 2001
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Planthopper Evolution(2001)
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Planthopper Evolution(2001) (2008)
XX
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Today
Ion Proton ($149,000)human genome for < $5,000, ~1 day (?)
MiSeq ($126,000)
Ion Torrent ($90,000)
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Planthopper Evolution
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Planthopper Evolution
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Planthopper Evolution
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Capillary sequencing
Sequencing by synthesis
Single molecule methods
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Planthopper EvolutionCapillary (Sanger) Sequencing
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Capillary (Sanger) Sequencing
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Fluorescence Important in (most) Next Gen Sequencing
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Planthopper EvolutionSteps Common to all Next Generation Sequencing Systems
1. Make Library:-- fragment DNA into unique fragments-- add custom adaptors (“linkers”)
2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
All sequence DNA in “massive parallel” fashion
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Planthopper EvolutionRoche/454 Sequencing
1. Make Library:-- fragment DNA into unique fragments-- add custom adaptors (“linkers”)
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Planthopper EvolutionRoche/454 Sequencing
2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
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Planthopper EvolutionRoche/454 Sequencing
2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
![Page 20: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/20.jpg)
Planthopper EvolutionRoche/454 Sequencing
2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
![Page 21: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/21.jpg)
Planthopper EvolutionRoche/454 Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
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Planthopper EvolutionIllumina Sequencing
1. Make Library:-- fragment DNA into unique fragments-- add custom adaptors (“linkers”)
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Planthopper EvolutionIllumina Sequencing
1. Make Library:-- fragment DNA into unique fragments-- add custom adaptors (“linkers”)
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Planthopper Evolution2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
Illumina Sequencing
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Planthopper Evolution3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
Illumina Sequencing
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Planthopper Evolution3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
Illumina Sequencing
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Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
1. Make Library:-- fragment DNA into unique fragments-- add custom adaptors (“linkers”)
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Planthopper Evolution2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
Life Tech/ABI Ion Torrent & Proton Sequencing
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Planthopper Evolution2. Amplify Library-- make many identical copies (“clones”) of each unique fragment-- copies are made on a solid surface
Life Tech/ABI Ion Torrent & Proton Sequencing
![Page 30: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/30.jpg)
Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
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Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
![Page 32: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/32.jpg)
Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
![Page 33: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/33.jpg)
Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
![Page 34: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/34.jpg)
Planthopper EvolutionLife Tech/ABI Ion Torrent & Proton Sequencing
3. Sequencing by Synthesis-- fragments are copied again (sequencing reaction)-- incorporation of each base “fires” a signal-- system detects signal coming from all clones “firing” at once for that unique fragment
![Page 35: DNA Sequencing Technology and its Applications in Evolution Research](https://reader036.vdocuments.mx/reader036/viewer/2022062408/56813c65550346895da5f407/html5/thumbnails/35.jpg)
Planthopper EvolutionSingle Molecule Systems: Pacific Biosciences
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Planthopper EvolutionSingle Molecule Systems: Oxford Nanopore
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Capillary sequencing
Sequencing by synthesis
Single molecule methods
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Planthopper EvolutionApplications of Next Generation Sequencing
Metagenomics
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Planthopper EvolutionApplications of Next Generation Sequencing
Microbiome
http://commonfund.nih.gov/hmp/
Human Microbiome Project
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Planthopper EvolutionApplications of Next Generation Sequencing
Microbiome
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Planthopper EvolutionApplications of Next Generation Sequencing
Bacterial Genome Sequencing
Bacteriome = insect organ made of bacteriocytes
Planthoppers
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Planthopper EvolutionApplications of Next Generation Sequencing
Ancient (=degraded) DNA Sequencing
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Planthopper Evolution
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Planthopper Evolution
Annual Review of Genomics and Human Genetics, 2008. 9: 387-402.
Youtube: Current Topics in Genome Analysis 2012; NHGRI Lecture Series.
-- Elaine Mardis-- Jonathan Eisen-- Julie Segre (Microbiome)
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Collaborators and Funding
Megan EhlersNCSU undergrad
Greg PahelNCMNS
Rob DunnNCSU
Holly MenningerNCSU
Dan FergusNCMNS
Megan ThoemmesNCSU undergrad
Jason CryanNCMNS
Julie HorvatnNCMNS