I have homologous sequences with more than 80% identity. I wonder these genes might have undergone gene duplication which resulted in their different activity (function), i.e. they are paralogs. I wanted to analyze whether gene duplication was the case. Is gene duplication event the only explanation for the divergence of two genes in their function yet sharing common origin? What other evolutionary event could have resulted in functional divergence (paralogous) of these two or more genes other than gene duplication?
Through phylogenetic analysis of these and other similar proteins from nearby species you may be able to understand if it is a duplication (and eventually when it happened) or an horizontal gene transfer event (but I don't know what organism are you speaking of so maybe it is not a possibility). Since the two copies are so similar, I would expect they are paralogs, therefore the result of a gene duplication event.
Hello Matteo, I have two genes from coffee with 90% identity. However, they diverged to have different function, are paralogs. I searched for homologous genes in related genomes (tomato and grapevine) and tried to detect gene duplication event using MEGA 7 software. The analysis doesn't show any gene duplication event in any of the genes from the three species. My question is what other possible evolutionary event can explain paralogous genes other than gene duplication?
take a look at the DGD, might help you.
http://dgd.genouest.org
fred
@Geleta. What do you mean there is no signal for duplication in the tree? In plants, 2 genes with 90% identity most likely are duplicates. Other plant genomes also have two copies of this gene? The two coffee genes go together in the tree or they split with sequences from additional plants? are you checking the genomes that are most closely related to coffee?
How do you know the function has diverged? if this is the case you are in the right position to understand what are the residues involved i this change, I would bet that 90% identity at the nucleotide level means only a few non synonymous changes in the protein (and these should be responsible for functional change).
hello Matteo, MEGA 7 gene duplication analysis indicates no gene duplication though these genes are sharing high nucleotide identity. Further analysis by RDP4 shows some DNA segment exchange. I came to conclude that the genes are not duplicates but undergone genetic recombination/conversion. Her is the MEGA 7 phylogenetic tree attached, too. Let me get your analysis, thank you.
I don't know this analytical tool in mega7. And I am not very familiar with recombination/conversion mechanisms. How do you assign the label 5 or 11 to the genes in the phylogenetic tree? Also, without confidence values for internal nodes, it is hard to see if the tree is affordable or not.
Hello Matteo, thank you so much for your concerns. Screenshot of gene duplication analysis by MEGA 7 indicates FALSE for gene duplication detection. Here I attached a shot showing that. This tree is slightly different from the previous ME phylogenetic tree, because they are two different analysis outputs.
As I told you, I don't know how this is calculated. For what I understand it looks in the tree for branching points dividing the tree in subtrees containing all the species. Clearly this does not happen in your tree. But, it is a different sort of gene duplication he is looking for. It tells you that there is not a point in the tree where the ancestor had gene5-11 ancestor and the childs both gene5 and gene11. But I think the point was how the two copies in coffee originated. What I can say is that the tree can be divided in two halves, one containing 5c, 11c and 5t and the other 5g 11g and 11t. So i ask again, how the labels 5 and 11 were assigned? It may well be that 5G is instead a 11G, and 11C is in fact a recent paralog of 5C. in this case you would miss 5G and 11C. Grape genome is still evolving in databases and several cultivars have been sequenced. For instance the genome from FMACH was for a heterozygous cv, while the French one was for a highly homozygous cv. Clearly this affects the genome assembly. Many plants underwent genome duplication events and this is one of the main mechanisms to produce multiple gene copies and gene families. So, again, make sure you get all the homologous sequences by homology (not previous annotations unless they are of super-high quality like sometimes in arabidopsis).
anyway the important question is also the bootstrap (or probability) of each bifurcation in the tree.
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