How do we design fungal and plant gene cloning primers using BamHI and SalI restriction sites? What other additional sequence sites should be included and what about the gene sequences? Should we use the gene sequences as it is or do we need to remove a few from the start and at the end of the sequences (intron exon).
I am not totally sure what you mean by GFP-taggged primers, because your primers are not tagged with GFP, but you usually use the primer to clone your gene of interest in a vector already containing the GFP sequence (however there is also the possibilty you have a vector without GFP - then you have to clone both sequences into your vector).
How you design your primer would depend on the vector you use - you have the possibilty to have an N-terminal GFP or a C-terminal GFP-Tag. The most important thing is that you must have an ORF which encompasses your gene of interest + the GFP and the GFP has to be in frame with your gene of interest.
This means if you have a C-terminal GFP tag your primers must exclude the native stop codon - otherwise translation will stop there and the GFP is not attached to your protein.
If your have a N-terminal GFP tag the native start codon will not interfere with the attachment of the GFP to your protein, however I would only include it if the methionine it encodes is part of your mature protein.
When you create your primer I would recommend to include around 20 bp of your gene of interest + the restriction site (and make sure that your cloning in frame with your restriction site). If you want to digest your PCR product directly a would also recommend to add 3-4 additional bases 3'prime of the restriction site as the digestion will usually be more efficient in this case. If youu have additional questions feel free to ask. I hope this helps and good luck with cloning
Well, as presented this honestly reads more like a homework assignment than a research question. If it's not, my apologies.
Dörthe Andrea Kesper gave you some excellent parameters to follow for the overall cloning for a GFP fusion. Your advisor and other lab members are also excellent resources.
One thing that could help you to get more specific advice it to put in an image of your cloning vector and restriction sites. Also, if you are meant to use those specific restriction enzymes, double check to make sure their recognition sequences are absent from any genes to intend to clone with them.