title: Identification of mutations in evolved bacterial genomes.
abstract: Directed laboratory evolution is a common technique to obtain an evolved bacteria strain with a desired phenotype. This technique is especially useful as a supplement to rational engineering for complex phenotypes such as increased biocatalyst tolerance to toxic compounds. However, reverse engineering efforts are required in order to identify the mutations that occurred, including single nucleotide polymorphisms (SNPs), insertions/deletions (indels), duplications, and rearrangements. In this protocol, we describe the steps to (1) obtain and sequence the genomic DNA, (2) process and analyze the genomic DNA sequence data, and (3) verify the mutations by Sanger resequencing.
authors: Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.
authors: Liam
authors: L
authors: Royce
authors: Erin
authors: E
authors: Boggess
authors: Tao
authors: T
authors: Jin
authors: Julie
authors: J
authors: Dickerson
authors: Laura
authors: L
authors: Jarboe
mesh_terms: D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D019020:Directed Molecular Evolution; D020440:Gene Duplication; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D059386:Reverse Genetics; D012984:Software
chemical_list: D004269:DNA, Bacterial