Considerthe following phylogenetic tree a Determine whether

Considerthe following phylogenetic tree:

(a) Determine whether the following gene pairs are orthologs or paralogs: (i) Hsap3 and Mmus 1(ii) Hsap2 and Mmus 2

(b) You are writing a manuscript for publication. In the latest draft, one of your co-authors has written, “Using the BLOSSUM40 matrix, we determined that our proteins are 70% homologous.” What is wrong with this statement?

Duplication node Speciation node Eua ontoglires (supra mates) Schematic gene tree containing 2 species Hsap and Mmus (numbers point to different genes) Hsapl Mmus1 sap2 Hsap2\' Mmus2 Mmus2 Hsap3 Mmus3 Mmus3

Solution

Answer:

Orthologues:

Any gene pairwise relation where the ancestor node is a speciation event. We predict several descriptions of orthologues.

Paralogues:

Any gene pairwise relation where the ancestor node is a duplication event.

(a) (i) Hsap3 and Mmus1 are formed by duplication at the ancestral node. So, they are paralogs.

(ii) Hsap2 and Mmus2 share their common ancestor at a speciation node. So, they are orthologs.

(b) BLOSUM matrix is a substitution matrix used for sequence alignment of proteins.

BLOSUM stands for BLOcks SUbstitution Matrix.

In the latest draft, the word is BLOSSUM40 which is wrong. It should be replaced by BLOSUM40.