Introduction to Sequencing Genomes and their characteristics 2

Introduction to Sequencing

Genomes and their characteristics 2

Genome • • • Genome is the entirety of an organism’s hereditary information It is encoded either in the DNA or in the case of some viruses, in the RNA The genome includes both genes and noncoding sequences of DNA/RNA

Comparing Genomes 1 Brown, T. A. (2002). Genomes 2 (Oxford: Wiley Liss) , pp 29 -69 1

Prokaryotic Genomes are Compact

Introns are Absent in Prokaryotic Genomes

Very Few Repeats in Prokaryotic Genomes

Sequence a Genome Assemble the Genome Annotation Structural Annotation Functional Annotation Comparative Genomics View Results through Browser

Genome Sequencing • • Genome sequencing is the process of determining the exact order of bases (A, T (U), G and C’s) that make up an organism’s DNA/RNA This entails sequencing of the organism’s • chromosomal DNA • mitochondrial DNA • chloroplasts (plants)

Genome sequencing technologies 10

Sequencing Techniques 2 1 st Generation 2 nd Generation { 2 Shendure J, et al. (2008). Nature Biot. 26: 1135

Comparing the Next Generation Techniques 2 Sequencing by synthesis Emulsion PCR Bridge PCR 2 Shendure J, et al. (2008). Nature Biot. 26: 1135

454 sequencing 3 3 Marguiles M, et. al. (2005). Nature 437: 376

Pyrosequencing 4 ATP sulfurylase Luciferase 4 Ronaghi M, et. al. (1997). Anal. Biochem. 242: 84

Illumina/Solexa Method 5 Bentley DR, et al. (2008). Nature 456: 53 5

Sequence a Genome Assemble the Genome Annotation Structural Annotation Functional Annotation View Results through Browser Comparative Genomics

Genome Assembly 6 Assemblers (AMOS, Celera, Mu. MMer) Reference Genome 6 Chial H. (2008). Nature Edu. 1: 1