Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi
Michael McClelland,Liliana Florea,Kenneth E. Sanderson,Sandra W. Clifton,Julian Parkhill,Carol Churcher,Gordon Dougan,Richard K. Wilson,Webb Miller +8 more
TLDR
The Escherichia coli K-12 genome was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A and the genome of the close outgroup Klebsiella pneumoniae and a hypothetical ancestral state of genomic regions that differ between ECO and SAL cannot be inferred from the present data.Abstract:
The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL) and the genome of the close outgroup Klebsiella pneumoniae (KPN). There are at least 160 locations where sequences of >400 bp are absent from ECO but present in the genomes of all three SAL and 394 locations where sequences are present in ECO but close homologs are absent in all SAL genomes. The 394 sequences in ECO that do not occur in SAL contain 1350 (30.6%) of the 4405 ECO genes. Of these, 1165 are missing from both SAL and KPN. Most of the 1165 genes are concentrated within 28 regions of 10-40 kb, which consist almost exclusively of such genes. Among these regions were six that included previously identified cryptic phage. A hypothetical ancestral state of genomic regions that differ between ECO and SAL can be inferred in some cases by reference to the genome structure in KPN and the more distant relative Yersinia pestis. However, many changes between ECO and SAL are concentrated in regions where all four genera have a different structure. The rate of gene insertion and deletion is sufficiently high in these regions that the ancestral state of the ECO/SAL lineage cannot be inferred from the present data. The sequencing of other closely related genomes, such as S.bongori or Citrobacter, may help in this regard.read more
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Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Michael McClelland,Kenneth E. Sanderson,John Spieth,Sandra W. Clifton,Phil Latreille,Laura Courtney,Steffen Porwollik,Johar Ali,Mike Dante,Feiyu Du,Shunfang Hou,Dan Layman,Shawn Leonard,Christine Nguyen,Kelsi Scott,Andrea Holmes,Neenu Grewal,Elizabeth Mulvaney,Ellen E. Ryan,Hui Sun,Liliana Florea,Liliana Florea,Webb Miller,Tamberlyn Stoneking,Michael Nhan,Robert H. Waterston,Richard K. Wilson +26 more
TL;DR: The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A and Klebsiella pneumoniae as mentioned in this paper.
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Sequencing and comparison of yeast species to identify genes and regulatory elements
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Prophages and bacterial genomics: what have we learned so far?
TL;DR: In this paper, the evolution of integrated virus genomes (prophages) is analyzed using nucleotide sequence analysis, and it is shown that some prophages can lie in residence for very long times, perhaps millions of years, and that recombination events have occurred between related Prophages that reside at different locations in a bacterium's genome.
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Fast and reliable prediction of noncoding RNAs
TL;DR: All of the known noncoding RNAs and cis-acting elements with high significance are recovered and compelling evidence for many other conserved RNA secondary structures not described so far to the authors' knowledge is found.
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Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis
Howard Ochman,Nancy A. Moran +1 more
TL;DR: This work has shown that changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts.
References
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