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Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples.

Michael CA, Andrew NR - BMC Genet. (2010)

Bottom Line: We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group.Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Macquarie University, Sydney, NSW, Australia. camcon@ozemail.com.au

ABSTRACT

Background: It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment.

Results: We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.

Conclusions: Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.

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Non-metric Multidimensional Scaling (nMDS) plot of the Gene Cassette assemblage collected from five distances (0, 0.01, 0.1, 0.5, 1, 5 m labelled A-F inclusive) along the two transects (1 and 2) 10 metres apart.
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Figure 1: Non-metric Multidimensional Scaling (nMDS) plot of the Gene Cassette assemblage collected from five distances (0, 0.01, 0.1, 0.5, 1, 5 m labelled A-F inclusive) along the two transects (1 and 2) 10 metres apart.

Mentions: Initial analysis of the gene cassette size class data set showed that cassette size classes did not assort randomly (Table 2, p observed > = expected: < 0.0001). This was seen most clearly in the non-metric multidimensional scaling plot (Figure 1), where the degree of similarity of cassette populations between different sample sites mirrored their physical locations, thus showing relationship amongst sample sites. In order to further investigate this non-random arrangement of cassette size classes, a more detailed examination of the distribution was undertaken:


Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples.

Michael CA, Andrew NR - BMC Genet. (2010)

Non-metric Multidimensional Scaling (nMDS) plot of the Gene Cassette assemblage collected from five distances (0, 0.01, 0.1, 0.5, 1, 5 m labelled A-F inclusive) along the two transects (1 and 2) 10 metres apart.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2927473&req=5

Figure 1: Non-metric Multidimensional Scaling (nMDS) plot of the Gene Cassette assemblage collected from five distances (0, 0.01, 0.1, 0.5, 1, 5 m labelled A-F inclusive) along the two transects (1 and 2) 10 metres apart.
Mentions: Initial analysis of the gene cassette size class data set showed that cassette size classes did not assort randomly (Table 2, p observed > = expected: < 0.0001). This was seen most clearly in the non-metric multidimensional scaling plot (Figure 1), where the degree of similarity of cassette populations between different sample sites mirrored their physical locations, thus showing relationship amongst sample sites. In order to further investigate this non-random arrangement of cassette size classes, a more detailed examination of the distribution was undertaken:

Bottom Line: We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group.Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology, Macquarie University, Sydney, NSW, Australia. camcon@ozemail.com.au

ABSTRACT

Background: It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment.

Results: We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.

Conclusions: Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.

Show MeSH