Prediction of Evolutionary Relationship among different organisms on the basis of the presence of ‘Coagulation factor VIII’
Coagulation Factor VIII:

Factor VIII (FVIII) is an essential blood clotting factor. It is a glycoprotein procofactor synthesized and released into the bloodstream by the endothelium. In the circulating blood, it is mainly bound to von Willebrand factor to form a stable complex.
In humans, Factor VIII is encoded by the F8 gene. It is a cofactor for factor IXa which, in the presence of Ca+2 and phospholipids forms a complex that converts factor X to the activated form Xa. The Factor VIII gene produces two alternatively spliced transcripts. Transcript variant 1 encodes a large glycoprotein, isoform a, which circulates in plasma and associates with von Willebrand factor in a noncovalent complex. This protein undergoes multiple cleavage events. Transcript variant 2 encodes a putative small protein, isoform b, which consists primarily of the phospholipid binding domain of factor VIIIc. This binding domain is essential for coagulant activity.

Defects in this gene results in hemophilia A, a common recessive X-linked coagulation disorder.
Factor VIII can be used as an Anti-hemophilic factor to cure hemophilia. FVIII concentrated from donated blood plasma (Aafact), or alternatively recombinant FVIII can be given to hemophiliacs to restore hemostasis. Thus, FVIII is also known as Anti-hemophilic factor.[1][2]
To confirm the occurence of ‘Hemophilia A’ due to the defective ‘Coagulation factor VIII’, follow these steps:

Go to OMIM main page at http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM:

Search for “hemophilia A” by typing in “hemophilia A in the search field”:

This will give a list of texts available on hemophilia A:

Click on the first item, this will give the information found as literature :

This clearly states that hemophilia A, an X-linked recessive trait, is caused by mutation in gene coding for the “Coagulation factor VIII”:

Now working on this ‘Coagulation factor VIII’, we need to find the phylogenetic relationships among different organisms (mammals) based on the presence of this factor, follow these steps:
In NCBI:

Search “nucleotide” for “hemophilia A factor VIII” at NCBI at http://www.ncbi.nlm.nih.gov/:

Retrieve the sequence of “nucleotide in FASTA format” by selecting FASTA in the drop-down list of Display section:

Its FASTA format is retrieved as:

Now to obtain its peptide sequence, go to GenScan(a gene prediction tool )at http://genes.mit.edu/GENSCAN.html:

In its entry box, enter the obtained FASTA nucleotide sequence and “Run GenScan”. its peptide sequence can obtained as:

Now for “Run BLAST of this obtained peptide sequence”, for this go to “Expasy Proteomics Server” main page at http://www.expasy.ch/ :

Find BLAST in similarity search tools:

Enter the peptide sequence in the entry box of BLAST and run BLAST for similarity searches:

In UniProt:

An alternative for this could be by using “UniProt”, for this go to Uniprot at http://www.uniprot.org/ and type “human coagulation factor VIII” as a query. The Result would be:

Select the 1st one and click on BLAST option to run BLAST on it:

Running “BLAST at UniProt”:

The BLAST results will reveal the similarity of the ‘Human Coagulation factor’ with many ‘Factors VIII’ present in other different organisms:

Among them select only the factor VIII in other organisms:

After selection, retrieve their ‘sequences in FASTA format’ by clicking “Retrieve” :

Sequence of all selected sequences in FASTA is obtained as:

Now go to “Clustal W” at http://www.ebi.ac.uk/Tools/clustalw/:

Paste the sequences in FASTA retrieved from UniProt:

After choosing “Alignment as fast”, “output order as input” and “turning on the ignore gaps option” Run ClustalW. The results can be obtained as ‘Phylogram’, ‘DND file’, ‘Newick format’ and on ‘Jalview’ on Clustal W:

Show as phylogram tree:

The “Phylogram tree” on Clustal W:

“Phylogram with distances” on Clustal W:

Now for obtaining different types of phylogenetic trees(for prediction of evolutionary relationships), we need to get the phylogram in ‘Newick format’. For this, click to view the “DND file”:

PhyloDraw(a tool for construction of phylogenetic trees) can be downloaded from http://pearl.cs.pusan.ac.kr/phylodraw/. It takes input as ‘Newick format’ and gives output as various types of Phylogenetic trees. Open PhyloDraw:

Paste Newick format in a text file and save it, and open it file in PhyloDraw:

Click on options in menu bar for different types of trees:

Unrooted:

Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about common ancestry.

Rooted tree:

A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree.

Radial tree:

In the radial tree layout, a single node is placed at the centre of the display and all the other nodes are laid around it. The entire graph is like a tree rooted at the central node.

Cladogram:

A cladogram is a tree formed using cladistic methods. This type of tree only represents a branching pattern, i.e., its branch lengths do not represent time.Different types of cladograms can be constructed using this tool.

Rectangle cladogram:

Slated cladogram:

Phylogram:

A phylogram is a phylogenetic tree that explicitly represents number of character changes through its branch lengths.

Result:

The different types of pylogenetic trees have confirmed the close evolutionary relationship among different organisms on the basis of presence of the ‘Coagulation factor VIII’.

References:

http://en.wikipedia.org/wiki/Factor_VIII
http://ghr.nlm.nih.gov/gene=f8

Contributed by:Ayesha Yaqoob