Open AccessHighly accurate genome sequences of Escherichia coli K‐12 strains MG1655 and W3110
Author(s) -
Hayashi Koji,
Morooka Naoki,
Yamamoto Yoshihiro,
Fujita Katsutoshi,
Isono Katsumi,
Choi Sunju,
Ohtsubo Eiichi,
Baba Tomoya,
Wanner Barry L,
Mori Hirotada,
Horiuchi Takashi
Publication year - 2006
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb4100049
Subject(s) - indel , biology , genome , prophage , escherichia coli , genetics , whole genome sequencing , base pair , indel mutation , computational biology , dna , gene , bacteriophage , single nucleotide polymorphism , genotype
With the goal of solving the whole‐cell problem with Escherichia coli K‐12 as a model cell, highly accurate genomes were determined for two closely related K‐12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single‐nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino‐acid residue deletion, five amino‐acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per 13 000 bases) were mostly within portions sequenced with out‐dated technology based on radioactive chemistry.