Module IV: Taxon specific aspects of the  barcoding pipeline (Fungi) 29 th  November Pre-Conference Course Benjamin Stielo...
<ul><li>Sample types </li></ul><ul><li>Fresh specimens </li></ul><ul><li>Herbarium specimens </li></ul><ul><li>Actively gr...
<ul><li>Sample types </li></ul><ul><li>Fresh specimens </li></ul><ul><li>Herbarium specimens </li></ul><ul><li>Actively gr...
Sample types CBS Fungal Biodiversity Centre
<ul><li>DNA extraction </li></ul><ul><li>DNA extraction from fungal samples is relatively simple </li></ul><ul><li>Commerc...
<ul><li>Challenges (PCR) </li></ul><ul><li>Ribosomal genes are easy to amplify </li></ul><ul><li>Protein coding genes  can...
<ul><li>Challenges (PCR) </li></ul><ul><li>DNA elution volume  can be  critical (vs. PCR success) </li></ul><ul><li>Use po...
DNA-lab and Sequencing unit Project management Sequence editing and validation Private databases CBS Strain  selection New...
Outlook CBS Fungal Biodiversity Centre
Thanks for your attention! [email_address] CBS Fungal Biodiversity Centre
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Benjamin Stielow - Fungi

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Taxon specific aspects of the Fungi barcoding pipeline.

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Benjamin Stielow - Fungi

  1. 1. Module IV: Taxon specific aspects of the barcoding pipeline (Fungi) 29 th November Pre-Conference Course Benjamin Stielow CBS Fungal Biodiversity Centre
  2. 2. <ul><li>Sample types </li></ul><ul><li>Fresh specimens </li></ul><ul><li>Herbarium specimens </li></ul><ul><li>Actively growing culture </li></ul><ul><li>Lyophilized culture </li></ul><ul><li>Culture stored in liquid nitrogen </li></ul><ul><li>Soil, other environmental samples… </li></ul>CBS Fungal Biodiversity Centre
  3. 3. <ul><li>Sample types </li></ul><ul><li>Fresh specimens </li></ul><ul><li>Herbarium specimens </li></ul><ul><li>Actively growing culture (CBS barcoding) </li></ul><ul><li>Lyophilized culture (CBS barcoding) </li></ul><ul><li>Culture stored in liquid nitrogen (CBS barcoding) </li></ul><ul><li>Soil, other environmental samples… </li></ul>CBS Fungal Biodiversity Centre
  4. 4. Sample types CBS Fungal Biodiversity Centre
  5. 5. <ul><li>DNA extraction </li></ul><ul><li>DNA extraction from fungal samples is relatively simple </li></ul><ul><li>Commercially available kits are well suitable </li></ul><ul><ul><li>Genomed: Jetquick </li></ul></ul><ul><ul><li>Epicenter: Mastepure Yeast kit </li></ul></ul><ul><ul><li>Qiagen: DNeasy </li></ul></ul><ul><ul><li>EZNA: Forensic DNA kit </li></ul></ul><ul><ul><li>96-well Acroprep plates </li></ul></ul>CBS Fungal Biodiversity Centre
  6. 6. <ul><li>Challenges (PCR) </li></ul><ul><li>Ribosomal genes are easy to amplify </li></ul><ul><li>Protein coding genes can be difficult to amplify </li></ul><ul><li>PCR setup can be time consuming (fine tuning) </li></ul>CBS Fungal Biodiversity Centre
  7. 7. <ul><li>Challenges (PCR) </li></ul><ul><li>DNA elution volume can be critical (vs. PCR success) </li></ul><ul><li>Use powerful polymerases (e.g. Takara HS) </li></ul><ul><li>Use efficient PCR cyclers (e.g. Senso Quest) </li></ul><ul><li>Use additives: BSA and DMSO </li></ul><ul><li>Work in small sample volumes (12.5 μ l ) </li></ul><ul><li>Dimension: 96 or 384 well format </li></ul>CBS Fungal Biodiversity Centre
  8. 8. DNA-lab and Sequencing unit Project management Sequence editing and validation Private databases CBS Strain selection New Strains DNA extraction Collection Stock database PCR Cycle sequencing PCR check Sequence facility LIMS Raw data Editing Validation Unpublished Barcode Published Barcode Automated Blast Public Database(s) Redo management Release policy DNA-Bank
  9. 9. Outlook CBS Fungal Biodiversity Centre
  10. 10. Thanks for your attention! [email_address] CBS Fungal Biodiversity Centre

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