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DNA Barcoding

DNA Barcoding. Flora in our wetlands. Fox Battalion. Kamalpreet Kaur Shivanthi Opatha Mona Lau Jessica Jimenez Maria Panayi Alex Marshall. Aim:. To collect and analyze DNA sequences from plants in order to identify unknown species.

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DNA Barcoding

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  1. DNA Barcoding Flora in our wetlands.

  2. Fox Battalion. • KamalpreetKaur • ShivanthiOpatha • Mona Lau • Jessica Jimenez • Maria Panayi • Alex Marshall

  3. Aim: To collect and analyze DNA sequences from plants in order to identify unknown species. To determine whether DNA barcoding can be used successfully by non-experts to identity plants species in our local environment/park/wet lands and to determine whether DNA barcoding could be used to identify plant species and whether the plants are native to that specific area.

  4. Introduction • DNA barcodes are relatively short DNA or genomic sequences taken from a standard position in the genome. They are highly variable between different species and allow for 99% Accurate identification of a specimen.

  5. Karkarook Park. • Karkarook Park is located on Warrigal Road in Moorabbin close to Holmesglen. • An artificial wetlands and lake created by extracting sand between 1997 and 2001. • Fishing is possible, with Redfin perch and rainbow trout reported. • The park was revegetated with native plants. As such we expected to find mostly native plants growing in the park.

  6. Materials & Methods • Samples of plant tissue are collected from new growth parts of the plant such as new leaves to ensure the best chance of extracting DNA.

  7. Of the 13 plants collected 4 yielded enough DNA.

  8. DNA Extraction. • DNA is extracted from plant tissue • DNA is run on an Agarose gel to ensure successful extraction • DNA is then amplifyed by PCR

  9. Sequencing PCRed DNA is sent to Micromon, Monash University for Sequencing . • CGACGGCCAGTATGTCACCACAAACAGAGACTAAAGCAGGTGTTGGATTTCAAGCTGGTGTTAAAGATTATAAATTGACTTACTAC.......... • The Sequence is then compared against an online Database called blast and checked against a large database.

  10. Results • The Blast program gives a list of the most likely match allowing u to identify the plant. • Sample 6: • Scientific Name:Holcuslanatus • Common Name: Yorkshire Fog or Velvet Grass • Info:Holcuslanatus commonly known as a Yorkshire fog or Velvet Grass is a perennial grass. The specific epithet lanatus is Latin for “woolly” which describes the plant’s hairy texture. In part of northern Europe the grass is a common native grass species and a hardy pasture grass. Not native to Australia .

  11. Holcuslanatus

  12. Results • Data was uploaded onto the Atlas of living Australia web site. And can now be used as a refference for future studys in the area.The Atlas is part of a worldwide effort to Barcode all living organisms on earth.

  13. Disscussion • From 13 samples we were able to get 4 plants species DNA sequences during our DNA bar-coding project • From our results we were able to identify 4 plants species. They are HolcusLanatus or Yorksire fog, JuccusEffusus or Soft Rush , Plantagolamceolata or Ribwordplantain,andMedicagoTruncatula or Barrel clover.

  14. Discussion • This shows DNA barcoding can be used successfuly to identify plant species in Australia with a basic laborator by non experts. • Some of our samples were more difficult to extract DNA from. In the future we would investigate alternative methods of DNA extraction eg genomic DNA extraction kits. • One of our PCRs did not work due to a large amount of protein in the sample. To avoid this in the future a phenol chloroform extraction to denature the proteins can be used and PCR repeated.

  15. Discussion • All 4 of our samples were found to not be native to Australia. Not as surprising as we first thought given the difficulty of maintaining the wetlands in isolation from the rest of the surround area. Such as paddocks directly next to the park. • Given that nonexperts can now positively identify species it will be of great benefit to future conservation work. As an accurate record of what plants are growing in an area can be created and maintained by even a small group of nonexperts. • We can also determine if more invasive species are taking hold of an rea and what they have replace.

  16. Conclusion • In conclusion: We achieved our aims to use DNA barcoding and identify plants. • We did not need any expert knowledge, and only a basic laboratory set up. DNA sequencing was easy to outsource. • For future work more samples should be taken and more DNA extracted. We can improve on 4 out of 13 samples yielding DNA!

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