Question

A-E please

10. You inherit a sequencing machine and decide to sequence the genome of an animal. A. (2pts) What animal would you pick? Briefly explain why. B. (6pts) How would you find the protein-coding genes in a new genome sequence? Describe one computational method and one experimental method. C. (4pts) List 4 other DNA elements would you expect to find in a new genome in addition to protein-coding genes? D. (3pts) If you compared the chromosomal organization of dogs, cats, wolves, mice, puffer-fish and humans, which pair of animals would you expect to show the greatest degree of synteny? Explain your choice. E. (3pts) Why would you compare the mitochondrial genomes of closely related species and the ribosomal RNA sequences of more distantly related ones?

Answer 1

A.

Ans:

The animal of my choice will be one which possess simple genome, such as fish (puffer-fish).

The genome size of this fish is ~ 400Mbp. Hence it is comparatiely easy to sequence, assemble and analyze such genomes rather than more complex genomes like humans and other mammals, whose genome size is ~2.5billion bp.

B

Ans:

Computational method:

Deposit or upload sequence of genome to NCBI-ORF finder.

It will give you ORF sequence and its respective translation frame.

The ORF or potential protein coding region provided by ORF finder can be verified by

SMART BLAST or regular BLASTP.

Experimental method:

Once the protein-coding gene is predicted and verfied by computational method, its sequence can be retrived from NCBI.

Design primer against that particular gene, amplify, clone, sequence to confirm the identity of the gene.

It is then followed by overexpression, purification and indentification of coding proteins by BLASTp.

C

Ans:

The new sequenced genome is expected to contain following elements apart from protein coding genes;

Insertion sequence

Transposons

non-coding region/DNA

Tandem repeats

D

Ans:

Amongst the list given

dog-wolves will show greatest degre of synteny, since they belong to same clade or class or cluster (i.e. they are phylogenetically related).

E

Ans:

The mitochondrial DNA has elevated mutation rate, and it does not show process of genetic recombination as that of other DNA in a cell and they are also inherited maternally. Moreover mitochondrial DNA are subjected to fast evolution. Due to these reasons they can be used to compare the two closely related species. It is thought that closely related species may have other genetic material similar, but mitochondrial DNA will not be same.

The ribosmal RNA was checked for distantly related species because rRNA is known to possess some constant region domain and some variable domain. The constant region domain is conserved throughout the species, whereas the variable region is not same. Hence on the basis of this variable rRNA domain the distantly related species are comapred.