Multiple Transfer Events Research Articles

Increased Prevalence of Salmonella Infantis Isolated from Raw Chicken and Turkey Products in the United States Is Due to a Single Clonal Lineage Carrying the pESI Plasmid.

Infantis has recently become one of the most common serotypes of Salmonella isolated in the U.S. from raw meat samples collected in processing facilities and in retail stores. Investigations have determined that the majority of these isolates contain the pESI plasmid, but there has not been a large-scale investigation of the chromosome of these isolates. Here, we investigated 3276 whole-genome sequences of Salmonella Infantis with and without the pESI plasmid to understand chromosomal differences between plasmid carriage groups. S. Infantis genomes arranged into multiple clades with a single clade containing the isolates carrying the plasmid. Fifty-eight SNPs were identified in complete linkage disequilibrium between isolates that did and did not carry the plasmid. However, there were no unique genes present only in the genomes of isolates containing the plasmid. On average, isolates with the plasmid did contain more insertion sequences than those without (p < 0.05). Given that S. Infantis isolates carrying pESI form a single clade, it can be inferred that the increase in carriage of this plasmid in the U.S. is due to rapid clonal expansion of a single strain rather than as a result of multiple transfer events. As this S. Infantis clone does not contain any unique chromosomal genes, its proliferation appears to be due to pESI plasmid-encoded genes that may be advantageous in the chickens and turkeys or in their environment.

Prediction of Aquaporin Function by Integrating Evolutionary and Functional Analyses

Aquaporins (AQPs) are a family of channel proteins, which transport water and/or small solutes across cell membranes. AQPs are present in Bacteria, Eukarya, and Archaea. The classical AQP evolution paradigm explains the inconsistent phylogenetic trees by multiple transfer events and emphasizes that the assignment of orthologous AQPs is not possible, making it difficult to integrate functional information. Recently, a novel phylogenetic framework of eukaryotic AQP evolution showed congruence between eukaryotic AQPs and organismal trees identifying 32 orthologous clusters in plants and animals (Soto et al. Gene 503:165-176, 2012). In this article, we discuss in depth the methodological strength, the ability to predict functionality and the AQP community perception about the different paradigms of AQP evolution. Moreover, we show an updated review of AQPs transport functions in association with phylogenetic analyses. Finally, we discuss the possible effect of AQP data integration in the understanding of water and solute transport in eukaryotic cells.

Following the transfer of DNA: How far can it go?

The issue of DNA transfer is becoming increasingly important in crime scene situations, as DNA analytical techniques now detect tiny amounts. Whereas primary and secondary DNA transfers have been well studied, subsequent transfer steps have received much less focus. This study aimed to measure the detectability of a DNA source after multiple transfer events. Transfer of wet blood gave a full genetic profile well beyond the secondary transfer events on both cotton and glass substrates. Dry blood gave a full profile well beyond the secondary transfer events on glass only, but to a lesser extent than wet blood. Touch DNA only produced a full profile on the primary substrate on both cotton and glass, and detectable quantities beyond the secondary transfer event on glass only. Our results will contribute to a better understanding of the tertiary and subsequent transfer of DNA, which will allow for improved evaluation of the likelihood of alternative scenarios explaining why an individual's DNA was found at a crime scene.

Phylogenomic approaches underestimate eukaryotic gene transfer

Phylogenomic approaches have shown that eukaryotes acquire genes via gene transfer. However, there are two fundamental problems for most of these analyses; only transfers from prokaryotes are analyzed and the screening procedures applied assume that gene transfer is rare for eukaryotes. Directed studies of the impact of gene transfer on diverse eukaryotic lineages produce a much more complex picture. Many gene families are affected by multiple transfer events from prokaryotes to eukaryotes, and transfers between eukaryotic lineages are routinely detected. This suggests that the assumptions applied in traditional phylogenomic approaches are too naïve and result in many false negatives. This issue was recently addressed by identifying and analyzing the evolutionary history of 49 patchily distributed proteins shared between Dictyostelium and bacteria. The vast majority of these gene families showed strong indications of gene transfers, both between and within the three domains of life. However, only one of these was previously reported as a gene transfer candidate using a traditional phylogenomic approach. This clearly illustrates that more realistic assumptions are urgently needed in genome-wide studies of eukaryotic gene transfer.

An acquisition account of genomic islands based on genome signature comparisons.

BackgroundRecent 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.ResultsOf 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 VvI-3 and VvI-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.ConclusionFrom 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.

Complex Histories of Genes Encoding 3-Hydroxy-3-methylglutaryl-CoenzymeA Reductase

The mevalonate pathway for the synthesis of isoprenoids can be found in organisms from all domains of life. It has been previously demonstrated that the first gene specific to that pathway, which encodes the enzyme 3-hydroxy-3-methylglutaryl-CoenzymeA reductase (HMGR), has been transferred between domains by lateral gene transfer on several occasions. Here we look within the domain Bacteria at lateral acquisition of HMGR, whether as a single gene or as part of a mevalonate pathway cluster. We observe a complex history of multiple transfer events probably reflecting the fact that HMGR could be beneficial in a variety of physiological and genetic contexts. We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection.