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Analysis of Current Pre_GI Content – Islandomics
When antibiotics became industrially produced following World War II, our quality of life and our longevity improved enormously. No one thought bacteria were going to become resistant. Bonnie Bassler The collection of all islands and island content aords the ability to do large scale analysis on islands and MGE as entities. The global analysis of islands enhances current knowledge and understanding of these elements as individuals and the communities they occupy. It may be possible to isolate islands from the host and regard them as living entities of their own residing in a host. Collections or groupings of islands may therefore be regarded as communities. The wealth of information available in Pre_GI oers researchers the opportunity to investigate these island communities.
The following sections aim to illustrate the application of Pre_GI with regards to future research made possible by the gathering of all island information in a single, accessible location.
Database introspection
The fate of an acquired island in a host may follow dierent paths. One such avenue would be fragmentation of the island as it has been proposed that after insertion certain islands may undergo cleavage. The availability of multitudes of islands and the compositional similarity between them as provided by the Pre_GI database enables investigation into the process of fragmentation after insertion. Empirical observations suggested that islands fragmented from a large insert would share compositional similarity of at least 80% and that the change in distance of OUP from the island to the host should not exceed 15%. Exclusion of islands with highly similar OUP to that of the host is forced by the mechanism of amelioration. All foreign DNA inserts are inuenced by amelioration and after time all islands composition reect that of the host and each other independent of the origin of the island. Within the set thresholds it was possible to isolate up to 10 groups of islands with distinct origins per host genome as shown in Figure 43. Host genome is represented by a data point with counts of predicted islands on the y-axis and number of distinct origins of the islands depicted on the x-axis.
It was found that the amount of islands predicted per genome was independent of the number of origins of the islands in the genome. 64 Islands found in Stigmatella auranti- aca DW4_3_1 displayed uniform DNA composition and thus possibly resulted from the fragmentation of a large insertion. This is equivalent in the 54 islands of Clostridium sac- charoperbutylacetonicum N1-4(HMT) and 52 islands of Clostridium pasteurianum BC1.
Motley islands in genomes resulting from at least 10 dierent origins are presented in Table 7. Hosts acquiring genes from variable sources included multiple symbiotic/pathogenic organisms and extremophyles dened by unusual enzymatic activities which may result from the solution of genes from distinct origins.
Relational links total 69,176,627 for OUP similarity above 75% and 3,692,401 for BLASTN similarity with an e-value threshold of 10?6. This relates to each island displaying compositional similarity to 2,586 and sequence similarity to 138 other islands with analogous or dissimilar hosts. Comparing the amount of compositional and sequence similarity links per islands reveals 2 distinct groupings of islands (Figure 44). These groups indicate a cluster of islands with a relatively small amount of BLASTN links (in average 150) and another cluster with a multiple BLASTN links (in average 1,500). The latter grouping indicates highly conserved sequences observed in islands, e.g. tRNA, ribosomal RNA, genes encoding gyrase subunits, etc.
The extensive amount of OUP links between islands in relation to the amount of BLASTN links between islands is not unexpected. Fragmentation of former larger segments or entities (integrated plasmid, phage or transferred DNA region) would indicate shared OUP similarity due to the common origin even though no homologous genes are shared between islands. In Figure 44 the grouping rich in BLASTN links (lower right) includes tRNA regions. Genes for tRNA are known as routine recombination attachment ( attP) sites targeted by phage and conjugative plasmid integrases [62]. These areas or sites are accepted to be excluded from HT events yet are included in the SWGIS island sequence as the sliding window approach is unable to separate foreign genomic material from the insertion (attP) sites. The commonality of these attachment sites in dierent islands is a clear indication of homology of these MGE.
The large constituent of OUP similarity links (69,176,627) in islands enables research on similarity between islands in taxonomic groupings. All OUP records were assembled in such a fashion to distinguish between links found for islands within the same genome, amid dierent strains of the same species, between dierent species of the same genus and so forth up the taxonomic pyramid ending in domain. Results are displayed in Figure 45. The general trend observed is that of a diminishing average value of OUP similarity values amid distantly related groups.
1 Chapter 1: Introduction
1.1 The Original Horizontal Transfer Event
1.1.1 Symbiogenesis or Endosymbiotic Theory
1.1.2 Alternate Endosymbiotic Theory: The Third Wheel .
1.1.3 Secondary and Tertiary Endosymbiosis: Matryoshka dolls
1.2 Prokaryote Horizontal Transfer
1.3 Mechanisms, Incorporation and Barriers of Prokaryotic Horizontal Transfer
1.4 Interdomain Horizontal Transfer
1.5 Transfer, transfer everywhere
1.6 Identication of Horizontal Transfer Events and Islands
1.7 Current Island Databases
1.8 Need for a Novel Database?
1.9 Ontology and Stratigraphy
1.10 Aims and Objectives
1.11 Discussion
2 Chapter 2: Optimization of composition-based island prediction and collection
2.1 SWGIS overview
2.2 SWGIS parametric optimization
2.3 SWGIS failures and problem resolving strategies
2.4 Continued analysis after prediction .
2.5 SWGIS comparison
2.6 Discussion
3 Chapter 3: Database construction, maintenance and expansion
3.1 Database Blueprint
3.2 A Table in every Room
3.2.1 Table: host
3.2.2 Table: host_information
3.2.3 Table: host_taxonomy
3.2.4 Table: island
3.2.5 Table: paidb and islandviewer
3.2.6 Table: blast_island .
3.2.7 Table: swgis_parameters
3.2.8 Table: swgis_parameters
3.3 Floating foundation
3.4 Maintenance and Expansion of Database
3.5 GUI development – open house for viewing
3.6 Discussion
4 Chapter 4: Pre_GI
4.1 Current Content
4.2 Cluster representative example
4.3 Gene annotation example
4.4 Locational search example .
4.5 Novel island(s) search and analysis U7
4.6 Discussion
5 Chapter 5: Analysis of Current Pre_GI Content – Islandomics
6 Chater 6: Case Studies and Applications
7 Chapter 7: Discussion
