Sequencing a myxo

Post Reply
User avatar
John
Site Admin
Posts: 59
Joined: Mon Jun 26, 2017 7:15 pm
Location: UK

Sequencing a myxo

Post by John » Sat Dec 09, 2017 5:31 pm

This may be a little ambitious but this is what is required. "Myxomycetes" by Stephenson and Rojas provides very good information of the subject. See Chapter 3 by Leontyev and Schinttler, p83.

1)Obtain sequences of myxomycete DNA

  • Use spores from mature sporangia and extract using a commercially available kit (homogenise, extract, centrifuge)
    Expand DNA using PCR (see note regarding primers)
    Run PCR products on gel to confirm success of reaction
    Purify PCR products using commercial kit
2) Sequence the DNA (Sanger method)
This can be done commercially

3) Compare sequence to existing sequences eg GeneBank, BLAST

Problems to overcome
Choose the correct sequence of primer for PCR (according to the group to be sequenced e.g. Lamproderma).
Get primer made commercially

Equipment needed
Correct primers
Gel electrophoresis
(Centrifuge)
DNA extraction kit
DNA purification kit

User avatar
John
Site Admin
Posts: 59
Joined: Mon Jun 26, 2017 7:15 pm
Location: UK

Re: Sequencing a myxo

Post by John » Sat Dec 09, 2017 5:58 pm

This seems like a neat way to extract the DNA without the need for a centrifuge

http://www.primerdesign.co.uk/products/ ... se-options

User avatar
John
Site Admin
Posts: 59
Joined: Mon Jun 26, 2017 7:15 pm
Location: UK

Re: Sequencing a myxo

Post by John » Sat Dec 09, 2017 6:23 pm

Primer information for Lamprodermas Fig S1 A

18S rDNA Phylogeny of Lamproderma and Allied Genera (Stemonitales, Myxomycetes, Amoebozoa)
Anna Maria Fiore-Donno, Akiko Kamono, Marianne Meyer, Martin Schnittler, Manabu Fukui, Thomas Cavalier-Smith, 2012

Available from: https://www.researchgate.net/publicatio ... _Amoebozoa [accessed Dec 09 2017].

Post Reply