Different alleles or paralogs?

Question

[ann-katrin.llarena]

Hei!

This is a bit of a newbie question, but here goes anyway.

I did a tblastn search for seven genes (one against one) for a range of bacillus genomes (all refseq for bacillus sens latu). I found that five of the genes are conserved, but two of the genes come in two different variants that kind of follow eachother. Meaning that the strains either have variant x1/x2 or y1/y2 of the two genes. They seem to be in the same loci on the genomes (inbetween the other genes) every time.

My question is: how do I know if these genes are alleles of the same loci, or actually paralogs? The pident between form x1 and y1 is 40-42%, and between y1 and y2 something like 50%. This varies quite alot from the remainder of the genes in the genecluster of interest, where variability is around 70-90% pident between the strains, including these with different x and y forms.

My post is probably very difficult to understand, but I am basically just trying to understand how you can actually get paralogs occupying the same site on a genome...copy, then delete seems a bit weird. And also how you would for procaryotic diverse species draw the line between a allele variation and homologs.

Thanks in advance, and look forward to your comments.

[ann-katrin.llarena]

Thank you ! I came to the conclusion that the variation is due to homologous recombination between different strains and that of course they are two different genes occupying the same space but with different function. Thanks! :)

Answer 1

[Vitis]

Technically, bacteria is "haploid", which means you can't have two "alleles" at the same locus. But biology always has exceptions. Sometimes, you have bacteria cells with multiple chromosomes, and at the same locus, the chromosomes can have different versions of the same gene. I think you'll have to figure this out based on the complete chromosome assemblies in these bacteria.