The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

Ricker, Nicole; Qian, Hong; Fulthorpe, Roberta R.

doi:10.1016/j.ygeno.2012.06.009

Cited by 73 publications

(57 citation statements)

References 36 publications

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“…Unfortunately, partial IS element hits upstream of a gene must therefore be interpreted with caution and cannot necessarily be attributed to actual presence of an IS element. It is known that repetitive sequences impede de novo genome assembly using short reads and result in fractured assemblies [24]. In testing assemblies from simulated reads derived from a finished reference genome 25%e77% of non-reconstructable genes were tagged as transposase-or IS-related, depending on the read length simulated [25].…”

Section: Discussionmentioning

confidence: 99%

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

et al. 2015

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Section: Discussionmentioning

confidence: 99%

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

et al. 2015

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“…However, several drawbacks of using genomic sequences for taxonomic purposes have been highlighted. Criticism emerged regarding the overrepresented sequences from bacterial species of medical or technological interest in comparison to other species (267), the lack of sequenced genomes from many strain types (252), the questionable quality of some genome sequences available in public databases (274), and the high proportion (63%) of presumably less informative draft genomes compared with complete genomes (275).…”

Section: From Culturomics To Taxonogenomicsmentioning

confidence: 99%

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

et al. 2015

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SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

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“…Consequently, most genomes are not completely resolved; they are submitted as draft genomes, often containing hundreds of contigs that are generally unannotated or poorly annotated [15]. As a result, many of these genomes are of limited use for comparative, functional, clinical and epidemiological studies [16]. In contrast to other methods, the Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing platform [17] can produce read lengths of up to 30,000 bp that are capable of spanning large repeat regions (such as rRNA operons), thereby facilitating the generation of complete genome assemblies without the need for additional sequencing.…”

Section: Introductionmentioning

confidence: 99%

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

et al. 2014

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Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

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The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

Cited by 73 publications

References 36 publications

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

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