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The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2

Overview of attention for article published in BMC Genomics, June 2015
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  • Good Attention Score compared to outputs of the same age and source (76th percentile)

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6 X users
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1 Wikipedia page

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56 Dimensions

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Title
The Streptomyces leeuwenhoekii genome: de novo sequencing and assembly in single contigs of the chromosome, circular plasmid pSLE1 and linear plasmid pSLE2
Published in
BMC Genomics, June 2015
DOI 10.1186/s12864-015-1652-8
Pubmed ID
Authors

Juan Pablo Gomez-Escribano, Jean Franco Castro, Valeria Razmilic, Govind Chandra, Barbara Andrews, Juan A. Asenjo, Mervyn J. Bibb

Abstract

Next Generation DNA Sequencing (NGS) and genome mining of actinomycetes and other microorganisms is currently one of the most promising strategies for the discovery of novel bioactive natural products, potentially revealing novel chemistry and enzymology involved in their biosynthesis. This approach also allows rapid insights into the biosynthetic potential of microorganisms isolated from unexploited habitats and ecosystems, which in many cases may prove difficult to culture and manipulate in the laboratory. Streptomyces leeuwenhoekii (formerly Streptomyces sp. strain C34) was isolated from the hyper-arid high-altitude Atacama Desert in Chile and shown to produce novel polyketide antibiotics. Here we present the de novo sequencing of the S. leeuwenhoekii linear chromosome (8 Mb) and two extrachromosomal replicons, the circular pSLE1 (86 kb) and the linear pSLE2 (132 kb), all in single contigs, obtained by combining Pacific Biosciences SMRT (PacBio) and Illumina MiSeq technologies. We identified the biosynthetic gene clusters for chaxamycin, chaxalactin, hygromycin A and desferrioxamine E, metabolites all previously shown to be produced by this strain (J Nat Prod, 2011, 74:1965) and an additional 31 putative gene clusters for specialised metabolites. As well as gene clusters for polyketides and non-ribosomal peptides, we also identified three gene clusters encoding novel lasso-peptides. The S. leeuwenhoekii genome contains 35 gene clusters apparently encoding the biosynthesis of specialised metabolites, most of them completely novel and uncharacterised. This project has served to evaluate the current state of NGS for efficient and effective genome mining of high GC actinomycetes. The PacBio technology now permits the assembly of actinomycete replicons into single contigs with >99 % accuracy. The assembled Illumina sequence permitted not only the correction of omissions found in GC homopolymers in the PacBio assembly (exacerbated by the high GC content of actinomycete DNA) but it also allowed us to obtain the sequences of the termini of the chromosome and of a linear plasmid that were not assembled by PacBio. We propose an experimental pipeline that uses the Illumina assembled contigs, in addition to just the reads, to complement the current limitations of the PacBio sequencing technology and assembly software.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 101 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
Taiwan 1 <1%
Unknown 97 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 17 17%
Student > Master 14 14%
Researcher 13 13%
Student > Bachelor 12 12%
Professor 6 6%
Other 16 16%
Unknown 23 23%
Readers by discipline Count As %
Agricultural and Biological Sciences 34 34%
Biochemistry, Genetics and Molecular Biology 22 22%
Chemistry 5 5%
Immunology and Microbiology 3 3%
Environmental Science 2 2%
Other 9 9%
Unknown 26 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 6. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 February 2016.
All research outputs
#6,370,870
of 25,388,177 outputs
Outputs from BMC Genomics
#2,409
of 11,245 outputs
Outputs of similar age
#67,756
of 277,138 outputs
Outputs of similar age from BMC Genomics
#56
of 247 outputs
Altmetric has tracked 25,388,177 research outputs across all sources so far. This one has received more attention than most of these and is in the 74th percentile.
So far Altmetric has tracked 11,245 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done well, scoring higher than 78% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 277,138 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 75% of its contemporaries.
We're also able to compare this research output to 247 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.