[DIYbio] Re: Isolating sequences from scratch

Hi Nico,

 

I would suggest practicing the techniques on a readily available plant, like a cheap houseplant.   Once you can do library prep easily, then send for the target plant.   

 

Plants have large genomes, so doing the entire genome with the usual combination of PacBio/Illumina assembly would be expensive, in excess of $100K.  Instead, if you make a clone library you can identify the likely genomic fragment by doing a relatively inexpensive end-sequence for each clone and comparing it to the plant species with known genome sequence.  It is more of an exclusionary process:  you can eliminate the clones which are not likely to contribute to the trait.  For example, genes involved in central metabolism will not influence flower morphology.  The clones you are left with are the ones to focus on.  That;s the fun part: you can compare clone sequence to the many mRNA sequences of plants known to be expressed in flowers only (as opposed to leaves, roots, etc.)

 

As always, the more you can do yourself,  the cheaper it will be.  Library construction and plasmid prep can be done in your home or a community lab or school.  Sequencing will probably have to be sent out unless you know someone with a sequencer.

 

I am in th DC area - are you nearby?  I would be happy to show you how to make a library.  I do this very often.