BIOL321 Unit 4 Problem Set 7 13. The following is an alignment of genome sequenc

Question

BIOL321 Unit 4 Problem Set 7 13. The following is an alignment of genome sequences from individuals in a population. Each row is an individual except the bottom line which instead is a consensus sequence using IUPAC symbols (R = A or G, Y = C or T, S = G or C, W = A or T, K = GorT, M = A or C). (a) How many SNPs are in the alignment? (b) How many recombination hot spots? (c) How many haplotypes? 2 TGTATCGGATAGCTAGACCATTGTAGACTACGCGTCTCGATÁGACGATACGTGGTTGAATACCC TGTTTCGGATAGCCAGACCATTGTGGACTACGCGTCTCGATCGACGATACGTCGTTGAATACCC TGTTTCGGATAGCCAGACCATTGTGGACTACGCGTCTCGATCGACGATACGTCGTTGAATACCC TGTTTCGGATAGCCAGACCATTGTGGACTACGCGTCTCGATCGACGATACGTCGTTGAATACCO TGTATCGGATAGCTAGACCATTGTAGACTACGCGTCTCGATAGACGATACGTGGTTGAATACCO TGTATCGGATAGCTAGACCATTGTAGACTACGCGTCTCGATAGACGATACGTGGTTGAATACCC TGTWTCGGATAGCYAGACCATTGTRGACTACGCGTCTCGATMGACGATACGTSGTTGAATACCC

Explanation / Answer

a) SNPs are single nucleotide variation occuring at specific position in different individuals of a species.

The ones you have marked cross are actually SNPs because at these specific positions, nucleotides are different.

B) Recombination hot spots are specific areas in a sequence which exhibit elevated recombination rate than their surroundings.

There are many reasons causing recombination hotspots but the one most relevant here is presence of fragile sites.

Fragile sites are the one which are more prone to recombination, that means they will unsure recombination at the site they are present by forming a hairpin like structure during replications which induces breaks in the structure thus ensuring recombination.

Now these fragile sites can be identified by these trinucleotide repeats: CGG-CCG, GAG-CTG, GAA-TCC, GNC-NGC.

Whenever these sequences are found that means there will be break in the sequence and a fragile site is present thus recombination hotspot will be there.

c) Haplotypes- group of those alleles which are linked together and are inherited together. So the clusters of alleles which are similar in all strands will be the haplotypes.for eg TGT initial trinucleotide is Haplotypes.

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