After finishing genome assembly I got a lot of scaffolds. and I found two scaffolds that were supposed to be connected. So I want to verify if those scaffolds are neighbored in genome. When I ask my professor, he said that I can check using PCR and if two scaffolds are got connected using PCR it means those were actually neighbored in genome. But I didn't understand at all cause I'm just doing computational work in my lab. Is there anyone who can explain about it?
PCR is a method to produce copies from a template piece of DNA. To amplify a given piece of DNA one requires a little DNA oligonucleotide called a primer that binds the single-stranded template and allows the enzyme that does the actual amplification (polymerase) to bind. In the below picture the template is blue, the primers are yellow and purple and the polymerase would start amplifying at these yellow and purple sequences to eventually produce a double-stranded piece of DNA as seen in step 3. One requires both a forward (yellow) and reverse (purple) primer for a successful PCR amplification.
In your case, one would design a primer pair with the forward on scaffold A and the reverse on scaffold B in a way that the product would have a resonable size, e.g. like a few kilobases or so because that is still in a range that can be well amplified. Conventional PCR works up to a few kilobases. Longer products are also possible and require long-range PCR. In any case, if the two scaffolds are not in proximity, you would not get a PCR product because, as said above, a successful PCR requires that both the forward and reverse primer sucessfully amplify the template sequence. If you never heard of PCR, it is a bit difficult to get your head around the concept, but there is a lot of online material available on it. As jrj.healey said, once you have a PCR product, you could send this to Sanger sequencing in order to confirm that it indeed comes from the two scaffolds.