Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing.

Genome Research
Ole SkovgaardNiels Tommerup

Abstract

Whole-genome sequencing (WGS) with new short-read sequencing technologies has recently been applied for genome-wide identification of mutations. Genomic rearrangements have, however, often remained undetected by WGS, and additional analyses are required for their detection. Here, we have applied a combination of WGS and genome copy number analysis, for the identification of mutations that suppress the growth deficiency imposed by excessive initiations from the Escherichia coli origin of replication, oriC. The E. coli chromosome, like the majority of bacterial chromosomes, is circular, and DNA replication is initiated by assembling two replication complexes at the origin, oriC. These complexes then replicate the chromosome bidirectionally toward the terminus, ter. In a population of growing cells, this results in a copy number gradient, so that origin-proximal sequences are more frequent than origin-distal sequences. Major rearrangements in the chromosome are, therefore, readily identified by changes in copy number, i.e., certain sequences become over- or under-represented. Of the eight mutations analyzed in detail here, six were found to affect a single gene only, one was a large chromosomal inversion, and one was a large chrom...Continue Reading

References

Nov 11, 1989·Nucleic Acids Research·J GrimbergL Belluscio
Feb 14, 1968·Journal of Molecular Biology·S Cooper, C E Helmstetter
Apr 14, 1967·Journal of Molecular Biology·B L Brownstein, L J Lewandowski
Nov 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·C W Hill, B W Harnish
May 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·P Anderson, J Roth
Nov 1, 1994·Molecular Microbiology·U von FreieslebenM Schaechter
Sep 5, 1997·Science·F R BlattnerY Shao
Apr 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Magnus LundgrenRolf Bernander
Nov 2, 2004·Journal of Bacteriology·Shiguo ZhouDavid C Schwartz
Jun 2, 2006·Molecular Systems Biology·Koji HayashiTakashi Horiuchi
Jun 7, 2006·Annual Review of Microbiology·Jon M Kaguni
Nov 4, 2006·Proceedings of the National Academy of Sciences of the United States of America·Elisabeth KugelbergJohn R Roth
Apr 17, 2007·Nature Reviews. Microbiology·Melissa L Mott, James M Berger
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Feb 17, 2010·Nature Reviews. Microbiology·Tsutomu KatayamaKazuyuki Fujimitsu

❮ Previous
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Citations

Jul 31, 2013·Nature·Christian J RudolphRobert G Lloyd
May 18, 2013·Nature Reviews. Genetics·Sara Huston Katsanis, Nicholas Katsanis
Feb 14, 2012·Nucleic Acids Research·Jan-Peter van Pijkeren, Robert A Britton
Nov 15, 2011·Journal of Bacteriology·Peter L FreddolinoSaeed Tavazoie
Jul 26, 2012·Journal of Biomedicine & Biotechnology·Lin LiuMaggie Law
Jul 12, 2013·Future Microbiology·Kathryn T ElliottEllen L Neidle
Jan 17, 2013·Molecular Microbiology·Ling DengQunxin She
Jul 21, 2012·Molecular Microbiology·Erik A PelveRolf Bernander
Sep 6, 2014·Bioinformatics·Vinita Periwal, Vinod Scaria
Oct 23, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Seema Patel
Nov 8, 2016·Nature Biotechnology·Christopher T BrownJillian F Banfield
Mar 29, 2018·BMC Genomics·Erin E GillFiona S L Brinkman
Apr 19, 2018·Molecular Biology and Evolution·Darya AusiannikavaThorsten Allers
Apr 27, 2018·Environmental Microbiology·Stefan SpringHans-Peter Klenk
Dec 14, 2018·Nucleic Acids Research·Sarah L Midgley-SmithChristian J Rudolph
Apr 30, 2017·G3 : Genes - Genomes - Genetics·Sarah Milbredt, Torsten Waldminghaus
Nov 5, 2013·Nature·Michelle HawkinsThorsten Allers
May 24, 2018·The Journal of Cell Biology·Vincent AmarhDavid R F Leach
Dec 19, 2018·Frontiers in Microbiology·Matthias BruhnTorsten Waldminghaus
May 1, 2020·Frontiers in Microbiology·Aisha H SyedaChristian J Rudolph
Dec 29, 2019·BMC Bioinformatics·Mehwish NoureenMasanori Arita
May 10, 2020·Scientific Reports·Abdoul-Razak TidjaniPierre Leblond
Feb 6, 2017·Indian Journal of Microbiology·Anukriti Sharma, Rup Lal

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