the previous tree was rooted using the out group e1118.
Furthermore, the Ka/Ks of the gene was calculated using DNAsp, giving us a value of 0.009 which shows that there has been evolutionary pressure to conserve the ancestral state.
The negative selection is also shown by the alfa of the McDonald kreitman test: -0.400.
There seems to be a selection for the maintenance of dgoR, which make it even more intriguing that it gets inactivated as soons as the strain are evolved inside the mice gut.
The strain that did not exhibit the dgoR genes are:
O157:H7EDL933,O157:H7Sakai,O157:H7EC4115,O157:H7_EC4042,O157:H7_EC4045,O157:H7_EC4206,O157:H7_TW14588,b185 and ta447, all members of the phylogroup E
h296 member of the phylogroup B2
h605 and ta004 in the outgroup
To find out whether dgoR was conserved or not in the coli strains, i constructed a phylogeny based on the sequences of the 117 strains were the gene was present using simple neighbour joining. The first construction showed that the b108 had a really long branch, and after looking at the sequence, it became clear that the last 20bp of the gene was missing: it was completely aligned with the other sequences (with just the last 20bp missing), but finished with a N. therefore i used the last 20bp of ta014 to complete the genome as they were closely related.
I obtained the following phylogeny.
I checked the e118 sequence to see if there was a problem like with b108 but it didn’t.
I will now try to look at the mutations of the gene along the edges of the tree.
I helped Melanie in the making of libraries for 2 samples from the twins study. To compare the effectiveness of different indexes, we used two diffrent types of indexes for each sample:
library 1: 89013 + 2 classical indexes
library 2: 89013+ 2 XT indexes
library 3: 17357 + 2 classical indexes
library 4: 17357 + 1 XT index + 1 classical index
For each sample, 1 library was realised with the classical index, and with an assembly of indexes to check if the XT indexes were working with the regular protocol, as should the samples with the classical indexes.