207_2009_Lect_16Sixteen - 10/15/2009 Biology 207, 2009...

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10/15/2009 1 Biology 207, 2009 Lecture sixteen Wednesday, 21 October Bacterial genomics genome – the full complement of an organism’s genetic information chromosome(s) and plasmid(s) microbial genomics – the sequence and analysis of a bacterium’s genome (identification of the genes present, their organization, their function and their expression) rovides efinitive insight into an rganism’s provides definitive insight into an organism s function, its interaction with the environment, and its evolutionary history Chromosome In the same way that molecular biology, beginning in the 1950s, completely transformed biology in the second half of the 20 th century, microbial genomics (whole Plasmid Plasmid genome sequencing and analysis) , which began in 1995, will transform biology in the first half of the 21 st century. History of microbial genomics one of the youngest disciplines in microbiology began in 1995 with report of the sequence of the genome of Haemophilus influenzae strain Rd , a species of bacteria that caused most cases of juvenile meningitis in the U.S. f i s d l d i 990 before vaccine was developed in 1990 genome size, 1.8 Mb (1,830,138 bp) this was the first genome sequenced of a free-living organism (before that, virus genomes had been sequenced; e.g. in 1982, the sequence of the genome of bacteriophagelambda, 48.5 kb, was qg pg ,, reported) the success with H. influenzae demonstrated the effectiveness of “whole genome shotgun sequencing” as a method for sequencing large genomes. Whole genome shotgun sequencing start by growing up a culture of the bacterial strain of interest, and extract and purify its chromosomal DNA shear the DNA mechanically into small fragments clone the fragments into a sequencing vector (this is now a “library” of the DNA of the strain of interest) using sequencing primers complementary to the vector at the positions flanking the fragment insertion site, sequence the fragment DNA of each clone assemble the sequences of overlapping fragments (contigs) using computer algorithms that recognize and align identical overlapping sequences) close any gaps between contigs (PCR amplification and sequencing of the product) annotate – identify genes (orfs) and their functions (using e.g., BLAST searches in GenBank)
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207_2009_Lect_16Sixteen - 10/15/2009 Biology 207, 2009...

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