So I was recently taught cloning in plants and I came to wonder what is the need to first put the gene of interest in the entry vector plasmid and then the final vector plasmid before finally transforming agrobacterium? Can someone make it make sense to me?
If you mean the binary system using the Ti plasmid:
The main issue is that on the massive Ti plasmid there is a difficulty locating unique restriction sites (see section "Introduction of Genes into Plants by Using Agrobacterium"):
However, Ti plasmids are very large and T-DNA regions do not generally contain unique restriction endonuclease sites not found elsewhere on the Ti plasmid. Therefore, one cannot simply clone a gene of interest into the T-region. Scientists therefore developed a number of strategies to introduce foreign genes into the T-DNA. These strategies involved two different approaches: cloning the gene, by indirect means, into the Ti plasmid such that the new gene was in cis with the virulence genes on the same plasmid, or cloning the gene into a T-region that was on a separate replicon from the vir genes (T-DNA binary vectors).
Both of these approaches mentioned involve a two-step cloning procedure for using the entry vector to add the payload to the Ti plasmid.