ArticlePLoS computational biology2009
Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 10 citations in OpenAlex.
- The Role of Genomic Islands in the Pathogenicity and Evolution of Plant-Pathogenic Gammaproteobacteria.Microorganisms · 2025Review
- Responses of the bacterial community of tobacco phyllosphere to summer climate and wildfire disease.Frontiers in plant science · 2022Article
- Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum.PloS one · 2017Article
- Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.BMC research notes · 2014Article
- Leptospire genomic diversity revealed by microarray-based comparative genomic hybridization.Applied and environmental microbiology · 2012Article
- Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain.Applied and environmental microbiology · 2010Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray comparative genomic hybridisation (aCGH) provides an estimate of the relative abundance of genomic DNA (gDNA) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043) and Dickeya dadantii 3937 (Dda3937); and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE) Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.