Hello,
Does anybody know what phylogenetic reconstruction method is best suited to build a tree with palindromic sequences from several lines of the same Drosophila species?
I'm trying to sequence a gene family that is made up of two inverted, highly similar (>99%) coding copies separated by 2kb of intergenic DNA.
The upstream and dowstream sequences of one copy show a moderate degree of identity (>90%) when compared with their counterparts from the other copy.
In order to understand the origins and evolution of this gene family, I am interested in finding out how the flanking and coding regions align among themselves, (if, for example, upstream sequences from Copy 1 cluster all together, or on the contrary, they are more similar to upstream sequences of Copy 2 from the same strain).
Many thanks in advance!
I think you can extract separately all your coding sequences, and flanking sequences (not forget to indicate their numbers (Copy 1 & Copy 2), align them and make 2 (or 3 for each upstream and downstream flanking seq) separate phylogenetic trees by any method you prefer. Than you will be able to compare all trees. The important question is: what is the length of all regions and how many sequences do you have.
Hi Ilya,
Many thanks for you reply and my apologies for the delay.
I am currently working with 42 sequences and the total length I'm trying to reconstruct is up to 8 kb.
I am analyzing the following different parts separately.
-2 coding regions of 2 kb lenght.
-Flanking upstream DNA of each copy (about 1kb pb).
-Flanking downstream DNA (about 1 kb).
After comparing all trees using Neighbour-Joining, it seems that the coding regions and the upstream flanking regions closest to them are grouped according to the arrangement, while the rest don't show this pattern, or group according to the copy they belong to (C1 or C2).
I was thinking that maybe there's some concerted evolution going on, but I don't know how could I prove it, since the polymorphism level in the coding region is so low.
Kind regards
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics