ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

Glasner, Jeremy D.; Rusch, Michael; Liss, Paul; Plunkett, Guy; Cabot, Eric L.; Darling, Aaron E.; Anderson, Bradley D.; Infield-Harm, Paul; Gilson, Michael C.; Perna, Nicole T.

doi:10.1093/nar/gkj164

Cited by 57 publications

(47 citation statements)

References 16 publications

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“…The consensus sequence of the first complete (single-contig) assembly was imported into the Web-based ASAP database (15,16) to aid analysis and annotation by multiple users in different locations. Annotated Feature coordinates were updated when refinements to the assembly produced new genome versions.…”

Section: Methodsmentioning

confidence: 99%

The Complete Genome Sequence ofEscherichia coliDH10B: Insights into the Biology of a Laboratory Workhorse

et al. 2008

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Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B.Molecular biology studies rely heavily on Escherichia coli for essential operations, ranging from the simple propagation of plasmid DNA to the creation of large clone libraries for wholegenome sequence determination. Among the strains developed as hosts for these everyday applications, DH10B (17) is commonly used across the research community, taking advantage of particularly useful properties exhibited by the strain. These include high transformation efficiency, the ability to take up and stably maintain large plasmids, the lack of methylation-dependent restriction systems (MDRS), and colony screening via lacZ-based ␣-complementation. However, analysis of sequenced bacterial artificial chromosome (BAC) clones derived from DH10B shows a high incidence of insertion sequence (IS) transposition from the chromosome into the cloned fragment (25).The genome of DH10B was constructed before the modern era of molecular biology, through a series of genetic manipulations (Fig. 1). The progenitors were all K-12 strains, with the exception of D7091F, in which a region surrounding the ⌬(araA-leu)7697 deletion had been derived from E. coli B SB3118 by P1 transduction (John Wertz, personal communication). Ultimately, MC1061 (9) served as a starting point for Hanahan and coworkers to replace alleles by using a series of P1 transductions that resulted in DH10B (17). Among the engineered gene replacements were recA1 ...

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Section: Methodsmentioning

confidence: 99%

The Complete Genome Sequence ofEscherichia coliDH10B: Insights into the Biology of a Laboratory Workhorse

et al. 2008

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“…Increasingly, specific software packages are being developed substantially improving the way in which these datasets can be analyzed, including T-RFLP data (Marsh et al, 2000;Kent et al, 2003;Shyu et al, 2007), analysis of gels (e.g. Gelcompar), DNA array data (Allison et al, 2006), or genomics and proteomics in general (Zeeberg et al, 2003;Glasner et al, 2006). The ultimate goal is to understand and model the main dynamic interactions in complete microbial communities.…”

Section: Data Analysis and Interpretationmentioning

confidence: 99%

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

2008

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“…The confirmed hrpL up-regulated recombinant clones were end-sequenced using primers pPROBE-AT For/ Rev (Table 2) and compared with the Ech3937 genome sequence via ASAP (a systematic annotation package for community analysis of genomes http:// asap.ahabs.wisc.edu/asap/ASAP1.htm) to obtain the full-length DNA sequence of each insert (Glasner et al 2006). The individual promoter and ORF within the insert was obtained from ASAP, in which each gene was assigned a unique ASAP number.…”

Section: Sequencing and Annotating Hrpl Up-regulated Genesmentioning

confidence: 99%

Identification of hrpL up-regulated genes of Dickeya dadantii

Shi

Cooksey

2008

Eur J Plant Pathol

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Dickeya dadantii (Erwinia chrysanthemi) is a Gram-negative plant pathogen that invades a wide range of plant species to cause diseases. Hypersensitive response and pathogenicity genes (hrp) are important virulence factors in D. dadantii. However, few hrpL up-regulated genes of D. dadantii have been reported. In this study, a green fluorescence protein (GFP)-based Escherichia coli promoter-probe system was used to identify hrpL up-regulated genes in D. dadantii 3937. From approximate 20,000 library clones screened, hrpA, hrpK, dspE, yijC (a DNAbinding transcriptional regulatory protein) and yecF (unknown function) were identified to be up-regulated by hrpL in D. dadantii 3937. Expression pattern fluorescence of five genes was observed in the wildtype strain and a hrpL deletion mutant strain of D. dadantii 3937 in hrp-inducing minimal medium. Mutants with hrpA, hrpK, dspE, yijC, and yecF genes mutated, respectively, were confirmed, and most of the mutants showed virulence reduction when infecting the plant host African violet (Saintpaulia ionantha).

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ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

Cited by 57 publications

References 16 publications

The Complete Genome Sequence ofEscherichia coliDH10B: Insights into the Biology of a Laboratory Workhorse

The Complete Genome Sequence ofEscherichia coliDH10B: Insights into the Biology of a Laboratory Workhorse

Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

Identification of hrpL up-regulated genes of Dickeya dadantii

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