I am trying to understand the molecular evolution of a gene family that composes of only two members (let's say X1 and X2). I have looked into the genomic neighborhoods of X1 and X2 in various species using Genomic Alignments in Ensembl and constructed a genomic neighborhood illustration of other genes flanking X1 and X2. However, my Blast searches didn't detect X2 in some fish species. When I looked into the genomic neighborhood of X2 in these fish species, I saw another X1 like sequence instead. I am thinking that maybe X2 was converted into X1 after the duplication event, but how can I prove that? My assumption may be stupid because I am not very experienced with genetics and concepts of evolutionary biology, but any help would be appreciated.
Dear George ,
BLAST processes sequences and the prefix of X2 resembling X1 should not prevent the detection of X2 .
Since you are stating that X2 in fact occurs and that BLAST did not detect it there might be some mutations that occurred within X2 that caused the score of the hit to go down. It does not necessarily mean that X2 is converted to X1.
Try to alter the parameters of the search. Further, the absence of a hit for the sequence that you are searching does not mean an absence of the gene (in terms of genetic function).
Finally if the query exactly matches a part of X2 sequence and yet X2 is not reported then you identified a fault with the software.
Best regards.
Fishes have normally whole genome duplications making 2-4 copies of the genes, which may have single copy in human or say lampreys.
Duplicated genes need to adopt to new or sub-new functions, or else they will die or atleast one will not be present.
one way is look from different synteny viewers like ucsc genome browser, ensembl, NCBI map viewer.
Divide your objective into sub tasks
a) make a none-fish vertebrate synteny of X1 gene
b) make fish specific syntenies of gene X1a and X1b
c) Combine more features like sequence identity, sequence motifs and gene structure
d) look on the scale of 1 Mb size minimum,
it will become clear.
Look in my papers several of these papers deals with vertebrate wide genomic comparisons.
Your assumption is not stupid ! it could have occured but depending on the conservation you should get some info. Are the fish where you seem to have X1 instead of X2 in the X2 syntheny context related (could you tell if it occurred in a specific phyllum) You could also think that after the duplication from an ancestor that looks like X1. The X1 type is well conserved even if the synteny is changed but that in some fish the conservation of one copy is relaxed and the X1 evolved to be an X2. Depending on the number of taxa analysed which hypothesis would be more parcimonious?
Your assumption is reasonable. Another possibility is simply that one of the genes has been lost. Some fish species have had 2 rounds of genome duplications and afterwards lost some of the duplicated genes. Doing a synteny analysis, as Abhishek Kumar also recommended, would enable you to distinguish between gene loss and gene conversion.
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