Creating synthetic genomes Strategies for design and assembly

Synthetic Viruses Goal: Can we use synthetic genomics to reconstruct a historically important pathogen in order to study it and learn how pandemic influenza viruses originate? The 1918 Spanish flu

Strategy: Obtain the sequence of the virus genome Recreate the virus genome Study the virus

Recreating the virus genome

Studying the virus: What gene enables respiratory transmission? Infected ferrets Littermates When the 1918 PB 2 gene is added to a duck virus, that virus becomes capable of respiratory transmission

Synthetic Bacteria Goal: Can we use synthetic genomics to create the genome of a living organism and will that synthetic genome function in cells? Strategy: Create a complete chromosome in the lab from chemicals Watermark the DNA Use hierarchical assembly Insert synthetic DNA into cells and allow to make proteins Synthetic DNA “reprograms” cells-changes from one species to another

Strategies for designing a synthetic genome: Use of watermarks

Strategies for designing a synthetic genome: Hierarchical assembly D G Gibson et al. Science 2010; 329: 52 -56

Synthetic genome transplantation • Introduce synthetic M. mycoides genome from yeast into M. capricolum recipient • Screen for blue cells M. mycoides cells 00

DNA is software that creates its own hardware

Synthetic Yeast Goal: Can we use synthetic genomics to design a genome to learn about complex genomes? Strategy: Create a chromosome with substantial changes Watermark the DNA Use hierarchical assembly No changes to protein-coding regions but delete repetitive DNA Remove all TAG nucleotides Use the synthetic DNA pieces to sequentially replace the normal yeast chromosome from the same species

Strategies for designing a synthetic genome: Hierarchical assembly Narayana Annaluru et al. Science 2014; 344: 55 -58 Published by AAAS

The future? • Use of automation/ robotics to streamline and speed up process • Creating complete designed synthetic genomes • Creation of larger eukaryotic genomes • De-extinction scenarios (passenger pigeons, wooly mammoths…. )