A whole-genome phylogeny of the family Pasteurellaceae

I have been delaying the work on whole genome based phylogeny for almost two months but I have no escape now and had work on it. In principle it is pretty simple but data mining and formatting is itself a challenge. I will try to warm up by reading this article published in Molecular Phylogenetics and Evolution. This work in done Sackler Institute last year.

They have used 12 whole genome sequences with 3130 genes. It is shown that we should have at least 160 genes concatenated in order to produce reliable results. 

"More recent phylogenetic studies
(Christensen et al., 2004; Gioia et al., 2006; Redfield et al., 2006)
have included the added power of considering multiple genes in
phylogenetic analysis. With over 10 species of Pasteurellaceae with
whole-genome sequences it is now possible to use whole-genome
datasets to assess the evolutionary relationships in this family."

Here is a list of species used on article,


Here comes the tough part, following methods and material,
1. Matrix construction

Structure-Function Analysis of a CVNH-LysM Lectin Expressed during Plant Infection by the Rice Blast Fungus Magnaporthe oryzae

Hi Guys(probably only me :P),


This article was discussed in our group and worth mentioning a short review here. Just to start with if CVNH means Cyanovirin-N homolog proteins which are not very well studied. Here author talks about different types of CVNH and differentiate these on functional/structural basis. Here is type III domains of CVNH:


Both of the domains CVNH and LysM has been shown here to be Carbohydrate specific. Similarity between CVNH and LysM domain has been shown to argue for the similar function.






Further they have determined 3D NMR structure of this construct(MoCVNH-LysM).

That is all except more explanation on carbohydrate binding and for more details you can always refer to article.