TITLE

An acquisition account of genomic islands based on genome signature comparisons

AUTHOR(S)
van Passel, MWJ; Bart, A; Thygesen, HH; Luyf, ACM; van Kampen, AHC; van der Ende, A
PUB. DATE
January 2005
SOURCE
BMC Genomics;2005, Vol. 6, p163
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Recent analyses of prokaryotic genome sequences have demonstrated the important force horizontal gene transfer constitutes in genome evolution. Horizontally acquired sequences are detectable by, among others, their dinucleotide composition (genome signature) dissimilarity with the host genome. Genomic islands (GIs) comprise important and interesting horizontally transferred sequences, but information about acquisition events or relatedness between GIs is scarce. In Vibrio vulnificus CMCP6, 10 and 11 GIs have previously been identified in the sequenced chromosomes I and II, respectively. We assessed the compositional similarity and putative acquisition account of these GIs using the genome signature. For this analysis we developed a new algorithm, available as a web application. Results: Of 21 GIs, VvI-1 and VvI-10 of chromosome I have similar genome signatures, and while artificially divided due to a linear annotation, they are adjacent on the circular chromosome and therefore comprise one GI. Similarly, GIs Vv1-3 and Vv1-4 of chromosome I together with the region between these two islands are compositionally similar, suggesting that they form one GI (making a total of 19 GIs in chromosome I + chromosome II). Cluster analysis assigned the 19 GIs to 11 different branches above our conservative threshold. This suggests a limited number of compositionally similar donors or intragenomic dispersion of ancestral acquisitions. Furthermore, 2 GIs of chromosome II cluster with chromosome I, while none of the 19 GIs group with chromosome II, suggesting an unidirectional dispersal of large anomalous gene clusters from chromosome I to chromosome II. Conclusion: From the results, we infer 10 compositionally dissimilar donors for 19 GIs in the V. vulnificus CMCP6 genome, including chromosome I donating to chromosome II. This suggests multiple transfer events from individual donor types or from donors with similar genome signatures. Applied to other prokaryotes, this approach may elucidate the acquisition account in their genome sequences, and facilitate donor identification of GIs.
ACCESSION #
28858578

 

Related Articles

  • The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P. C. // PLoS Genetics;Aug2011, Vol. 7 Issue 8, Special section p1 

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity...

  • Functional Conservation of RNase III-like Enzymes: Studies on a Vibrio vulnificus Ortholog of Escherichia coli RNase III. Lee, Minho; Ahn, Sangmi; Lim, Boram; Lee, Dong-Ho; Lee, Kangseok // Current Microbiology;Apr2014, Vol. 68 Issue 4, p413 

    Bacterial ribonuclease III (RNase III) belongs to the RNase III enzyme family, which plays a pivotal role in controlling mRNA stability and RNA processing in both prokaryotes and eukaryotes. In the Vibrio vulnificus genome, one open reading frame encodes a protein homologous to E. coli RNase...

  • A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation.  // BMC Research Notes;2012, Vol. 5 Issue 1, p80 

    The article focuses on a study conducted to test various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes, which found that a cost-effective way for prokaryotic whole genome sequencing is a single end 454 Jr. run combined with a paired end 454 Jr. run. Solution to...

  • Complex prokaryotic genome structure: rapid evolution of chromosome II. Bavishi, Anish; Abhishek, Ankur; Lin, Lin; Choudhary, Madhusudan // Genome;Sep2010, Vol. 53 Issue 9, p675 

    Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with...

  • The Role of Reticulate Evolution in Creating Innovation and Complexity. Swithers, Kristen S.; Soucy, Shannon M.; Gogarten, J. Peter // International Journal of Evolutionary Biology;2012, p1 

    Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has...

  • Expression of Divergent LSU rRNA Genes in the Vibrio vulnificus CMCP6 Genome During Both Infection and Non-Pathogenic Stages. Hyun-Lee Kim; Sang-Mi Ryou; Minho Lee; Jin-Won Lee; Kangseok Lee; Jeehyeon Bae // Current Microbiology;Jan2011, Vol. 62 Issue 1, p133 

    The Vibrio vulnificus CMCP6 genome harbors nine copies of divergent large subunit (LSU) rRNA genes that may express and constitute four kinds of LSU rRNA molecules in a single cell. Primer extension analyses showed that these heterogeneous LSU rRNA transcripts are all expressed and assembled...

  • Hybrid Vibrio vulnificus. Bisharat, Naiel; Cohen, Daniel I.; Harding, Rosalind M.; Falush, Daniel; Crook, Derrick W.; Peto, Tim; Maiden, Martin C. // Emerging Infectious Diseases;Jan2005, Vol. 11 Issue 1, p30 

    The recent emergence of the human-pathogenic Vibrio vulnificus in Israel was investigated by using multilocus genotype data and modern molecular evolutionary analysis tools. We show that this pathogen is a hybrid organism that evolved by the hybridization of the genomes from 2 distinct and...

  • SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes. Gulig, Paul A.; de Crécy-Lagard, Valérie; Wright, Anita C.; Walts, Brandon; Telonis-Scott, Marina; McIntyre, Lauren M. // BMC Genomics;2010, Vol. 11, p512 

    Background: Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two...

  • Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae. Johnston, Calum; Caymaris, Stéphanie; Zomer, Aldert; Bootsma, Hester J.; Prudhomme, Marc; Granadel, Chantal; Hermans, Peter W. M.; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre // PLoS Genetics;Sep2013, Vol. 9 Issue 9, p1 

    Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics