Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
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).
Article activity feed
-
Now published in GigaScience doi: 10.1093/gigascience/giy015
Harry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeSion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner …
Now published in GigaScience doi: 10.1093/gigascience/giy015
Harry A. Thorpe 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Harry A. ThorpeSion C. Bayliss 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sion C. BaylissSamuel K. Sheppard 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel K. SheppardEdward J. Feil 1The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AYFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Edward J. Feil
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy015 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101033 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101034
-
-
