Hello.
Nowadays, I am studying on some proteins and their genes and their relationship, and their changes with evolution process.
Nowadays, I wonder how can I proof the gene disappearing process?
For example, there are three relative plants including "A", "B", and "C". According to the plant taxonomy, they are classified not in the same genus, but in the same tribe. In general theory, "A", "B", and "C" have a common ancestor, and "C" was divided first (older), than "A" and "B" were divided later (more recently). In the other words, "A" and "B" are closer to each other than "C".
However, a orthologs of protein X can be found in "A" and "C" but not in "B". Many researchers have studied protein X from the "A" plant, and the orthologous protein in the "C" plant. However, in "B" plant, the orthologous protein have not been reported and the gene locus have not been discovered. I had wanted to find it so I designed primers based on the sequence from "A" and "C" to obtain the sequence from "B", but it was failed.
How can I proof the gene lost at the "B" plant?
Hi Sang Heon,
Did you make the primers based on conserved regions between the orthologs? You can make degenerate primers from the orthologs if you need to.
Also, if you are looking for orthologous proteins with similar functions, you can try to generate antibodies that can bind to A and C and try to use it for testing of presence of the protein in B.
Thank you for your answer, Andika.
Many researchers including me would have tried a lot, but It have not solved yet. My conclusion is that there is no X protein in "B" because of gene lost with evolutionary process. So, I am wondering why and how it had been lost during the evolutionary process.
In my opinion, you may design degenerate primers by aligning not only the conserved regions of A and C but also some other very close relatives. We can not say the gene is lost just according to degenerate primers works or not.
Besides, It would be ambitious to say that the gene is lost. If you are interested in relatively close relatives, then you may first suspect that the gene can be silent in B. It means that gene exists but not active. You may simply look for the proteins with Western blot. If the protein results are positive, then you should check your degenerate primers if designed properly because it means that the gene is active and induced the protein replication. If the protein results are negative, there is the case of a silent gene.
My suggestion is that you do transcriptome analysis and compare with others' related regions. Of course, it is required a big budget and time but reliable. If you find the region in your result of target organism transcriptome, then silent gene case will be supported.
There is the other way which is CRISPR technology to turn on unexpressed, or “silent,” gene clusters in your target organism. Of course, you must spend time for optimisation of crisper conditions for your species and laboratory.
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