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The sequencing of genomes involves cutting chromosomes into fragments, sequencing the fragments, and then assembling the fragment sequences into continuous sequences for entire chromosomes. Current sequencing methods use automation and powerful computers. These methods use labeled nucleotides that are detected at the ends of growing polynucleotide chains.
learning outcomes
You should be able to:
Explain why overlapping sequence fragments are essential in sequencing genomes and how they are arranged to give the final sequence.
Identify the characteristics of open reading frames.
Describe exmples of comparative genomics.
In sequencing genomes, why are overlapping sequences obtained, and how are they arranged to give the final sequence?
Before sequencing, a long DNA molecule is cut into many fragments. These cuts are random (i.e., they are made at different random locations). The overlaps are important in arranging the final sequence. If there were only one type of cut, aligning the final sequence would not be possible. The sequences of the fragments are arranged by computer using the overlaps as a guide.
How are open reading frames recognized in a genomic sequence? What kind of information can be derived from an open reading frame?
Open reading frames are recognized by the presence of a promoter sequence, triplet start and stop codons, transcription termination sequence, and recognition sequences at the beginning and end of introns. The reading frame gives the promoter sequence (signal for when and where the gene is expressed) and the sequence of amino acids of the protein (an indication of its function).
What is comparative genomics? Give an example of how it is used.
Comparative genomics is the study of DNA sequences across different organisms. Similar sequences detected in different DNA samples may help reveal the function of a protein (when a sequence matches that of a known protein in another organism), the identity of a species known only by its DNA (metagenomics), and evolutionary relationships. The gene that influences the relative sizes of dogs, for example, was identified by comparative genomics.
The first genomes to be fully sequenced were those of viruses and prokaryotes. Next we will discuss the information provided by the relatively simple prokaryotic genomes.