Piggy: A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

Harry A. Thorpe; Sion C. Bayliss; Samuel K. Sheppard; Edward J. Feil

doi:10.1093/gigascience/giy015

Piggy: A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

Harry A. Thorpe
, Sion C. Bayliss
, Samuel K. Sheppard
, Edward J. Feil^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

51 Citations (Scopus)

Abstract

Background: The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences. Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

Original language	English
Pages (from-to)	1-11
Number of pages	11
Journal	GigaScience
Volume	7
Issue number	4
DOIs	https://doi.org/10.1093/gigascience/giy015
Publication status	Published - 1 Apr 2018

Bibliographical note

Funding Information:
The S. aureus genome sequences were generated as part of a study supported by a grant from the United Kingdom Clinical Research Collaboration Translational Infection Research Initiative and the Medical Research Council (grant G1000803, held by Sharon Peacock) with contributions from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate, on which E.J.F. was a principal investigator and S.C.B. was a postdoctoral researcher. H.A.T. is funded by a University of Bath research studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© The Author(s) 2018.

Keywords

Accessory genome
Bacteria
Gene expression
Genomics
IgMLST
Intergenic regions
Pan-genome
Staphylococcus aureus, Escherichia coli
Whole-genome sequencing (WGS)

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title = "Piggy: A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria",

abstract = "Background: The concept of the {"}pan-genome,{"} which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences. Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ({"}switched{"}) intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).",

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author = "Thorpe, \{Harry A.\} and Bayliss, \{Sion C.\} and Sheppard, \{Samuel K.\} and Feil, \{Edward J.\}",

note = "Funding Information: The S. aureus genome sequences were generated as part of a study supported by a grant from the United Kingdom Clinical Research Collaboration Translational Infection Research Initiative and the Medical Research Council (grant G1000803, held by Sharon Peacock) with contributions from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate, on which E.J.F. was a principal investigator and S.C.B. was a postdoctoral researcher. H.A.T. is funded by a University of Bath research studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} The Author(s) 2018.",

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T2 - A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

AU - Thorpe, Harry A.

AU - Bayliss, Sion C.

AU - Sheppard, Samuel K.

AU - Feil, Edward J.

N1 - Funding Information: The S. aureus genome sequences were generated as part of a study supported by a grant from the United Kingdom Clinical Research Collaboration Translational Infection Research Initiative and the Medical Research Council (grant G1000803, held by Sharon Peacock) with contributions from the Biotechnology and Biological Sciences Research Council, the National Institute for Health Research on behalf of the Department of Health, and the Chief Scientist Office of the Scottish Government Health Directorate, on which E.J.F. was a principal investigator and S.C.B. was a postdoctoral researcher. H.A.T. is funded by a University of Bath research studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © The Author(s) 2018.

PY - 2018/4/1

Y1 - 2018/4/1

N2 - Background: The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences. Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

AB - Background: The concept of the "pan-genome," which refers to the total complement of genes within a given sample or species, is well established in bacterial genomics. Rapid and scalable pipelines are available for managing and interpreting pan-genomes from large batches of annotated assemblies. However, despite overwhelming evidence that variation in intergenic regions in bacteria can directly influence phenotypes, most current approaches for analyzing pan-genomes focus exclusively on protein-coding sequences. Findings: To address this we present Piggy, a novel pipeline that emulates Roary except that it is based only on intergenic regions. A key utility provided by Piggy is the detection of highly divergent ("switched") intergenic regions (IGRs) upstream of genes. We demonstrate the use of Piggy on large datasets of clinically important lineages of Staphylococcus aureus and Escherichia coli. Conclusions: For S. aureus, we show that highly divergent (switched) IGRs are associated with differences in gene expression and we establish a multilocus reference database of IGR alleles (igMLST; implemented in BIGSdb).

KW - Accessory genome

KW - Bacteria

KW - Gene expression

KW - Genomics

KW - IgMLST

KW - Intergenic regions

KW - Pan-genome

KW - Staphylococcus aureus, Escherichia coli

KW - Whole-genome sequencing (WGS)

UR - https://www.scopus.com/pages/publications/85051575732

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DO - 10.1093/gigascience/giy015

M3 - Article (Academic Journal)

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AN - SCOPUS:85051575732

SN - 2047-217X

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SP - 1

EP - 11

JO - GigaScience

JF - GigaScience

IS - 4

ER -

Piggy: A rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

Abstract

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