Chapter 9, Problem 25P

Eukaryotic genomes are replete with repetitive sequences that make genome assembly from sequence reads difficult. For example, sequences such as CTCTCTCTCT .(tandem repeats of the dinucleotide sequence CT) are found at many chromosomal locations, with variable numbers (n) of the CT repeating unit at each location. Scientists can assemble genomes despite these difficulties by using the paired-end sequencing strategy diagrammed in Fig. 9.9. In other words, they can make libraries with genomic inserts of defined size, and then sequence both ends of individual clones.

Following are 12 DNA sequence reads from six cloned fragments analyzed in a genome project. 1A and 1B represent the two end reads from clone 1, 2A and 2B the two end reads from clone 2, etc. Clones 1–4 were obtained from a library in which the genomic inserts are about 2 kb long, while the inserts in clones 5 and 6 are about 4 kb long. All of these sequences have their 5′ ends at the left and their 3′ ends at the right. To simplify your analysis, assume that these sequences together represent two genomic locations (loci; singular locus), each of which contains a (CT)_n repeat, and that each of the 12 sequences overlaps with one and only one other sequence.

1A: CCGGGAACTCCTAGTGCCTGTGGCACGATCCTATCAAC

1B: AGGACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT

2A: GTTTTTGAGAGAGAGAGAGAGAGAGAGAGACCTGGGGG

2B: ACGTAGCTAGCTAACCGGTTAAGCGCGCATTACTTCAA

3A: CTCTCTCTCTCTCTCTCTCTCAAAAACTATGGAAATTT

3B: TAGTGATAGGTAACCCAGGTACTGCACCACCAGAAGTC

4A: GGCCGGCCGTTGTTGACGCAATCATGAATTTAATGCCG

4B: TCATGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA

5A: TAGTGCCTGTGGCACGATCCTATCAACTAACGACTGCT

5B: AAGGAAAGGCCGGCCGTTGTTGACGCAATCATGAATTT

6A: CAGCAGCTAGTGATAGGTAACCCAGGTACTGCACCACC

6B: GGACTATACGTAGCTAGCTAACCGGTTAAGCGCGCATT

a.	Diagram the two loci, showing the locations of the repetitive DNA and the relative positions and orientations of the 12 DNA sequence reads.
b.	If possible, indicate how many copies of the CT repeating unit reside at either locus.
c.	Are the data compatible with the alternative hypothesis that these clones actually represent two alleles of a single locus that differ in the number of CT repeating units?