Chapter 9.4: Sequencing Genomes

Question 1

Describe the hierarchical strategy

Answer 1

o They first separated the genome into large chunks by cloning 200-300 kb fragments in bacterial artificial chromosome (BAC) vectors, then they applied strategies to determine the order of the BAC inserts with respect to each other in the original genome. These methods allowed the researchers to determine the smallest set of BAC clones with the least amount of overlap that could cover the entire genome (the so-called minimal tiling path). The scientists then determined the DNA sequence of the entire insert in each BAC clone of the minimal tiling path so as to reconstruct the genome

Question 2

What were the four ideas behind Celera’s success?

Answer 2

 The term shotgun means that the insert fragments to be sequence are chosen randomly from the library without any prior characterization  To make the library, fragments of genomic DNA were generated by mechanical shearing of the DNA with sound waves (sonication). Random breakage of DNA ensures that the sequences of DNA from different fragments can overlap, allowing their assembly  The Celera researchers obtained two sequences from each clone, one from each end  The Celera scientists made three different genomic libraries that had different-sized inserts. They randomly sheared samples of whole-genome human DNA with three different levels of energy that allowed them to control the average size of the fragment produced.

Question 3

Describe the whole-genome shotgun strategy

Answer 3

o Determine DNA sequences, each about 1000 bases long, from random human genomic DNA inserts of millions of individual clones from a genomic library, and then look for overlaps between the sequences so that they can be assembled to reconstruct the sequence of the entire genome

Question 4

What is the one main advantage of the whole-genome shotgun strategy over the hierarchical approach?

Answer 4

• The whole-genome shotgun strategy has one main advantage with respect to the hierarchical approach: After the genomic libraries are constructed, the rest of the procedure can be highly automated