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New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

ABSTRACT: BACKGROUND: Human rhinoviruses (HRV), the most frequent cause of respiratory infections, include 99 different serotypes segregating into two species, A and B. Rhinoviruses share extensive genomic sequence similarity with enteroviruses and both are part of the picornavirus family. Nevertheless they differ significantly at the phenotypic level. The lack of HRV full-length genome sequences and the absence of analysis comparing picornaviruses at the whole genome level limit our knowledge of the genomic features supporting these differences. RESULTS: Here we report complete genome sequences of 12 HRV-A and HRV-B serotypes, more than doubling the current number of available HRV sequences. The whole-genome maximum-likelihood phylogenetic analysis suggests that HRV-B and human enteroviruses (HEV) diverged from the last common ancestor after their separation from HRV-A. On the other hand, compared to HEV, HRV-B are more related to HRV-A in the capsid and 3B-C regions. We also identified the presence of a 2C cis-acting replication element (cre) in HRV-B that is not present in HRV-A, and that had been previously characterized only in HEV. In contrast to HEV viruses, HRV-A and HRV-B share also markedly lower GC content along the whole genome length. CONCLUSION: Our findings provide basis to speculate about both the biological similarities and the differences (e.g. tissue tropism, temperature adaptation or acid lability) of these three groups of viruses.

SUBMITTER: Tapparel C

PROVIDER: S-EPMC1949831 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

Tapparel Caroline C Junier Thomas T Gerlach Daniel D Cordey Samuel S Van Belle Sandra S Perrin Luc L Zdobnov Evgeny M EM Kaiser Laurent L

BMC genomics 20070710

<h4>Background</h4>Human rhinoviruses (HRV), the most frequent cause of respiratory infections, include 99 different serotypes segregating into two species, A and B. Rhinoviruses share extensive genomic sequence similarity with enteroviruses and both are part of the picornavirus family. Nevertheless they differ significantly at the phenotypic level. The lack of HRV full-length genome sequences and the absence of analysis comparing picornaviruses at the whole genome level limit our knowledge of t ...[more]

PMID: 17623054

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Project description:BackgroundPhylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here.ResultsPhylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing the strong phylogenetic performance of random subsets of data also shown in this study. Phylogenetic results for both the 19-taxon and 44-taxon datasets corroborate previous hypotheses about the placement of Photobacterium and Aliivibrio within Vibrionaceae and also highlight problems with how Photobacterium is delimited and indicate that it likely should be dissolved into Vibrio to produce a phylogenetic taxonomy. The 19-taxon and 44-taxon trees based on the large chromosome are congruent for the majority of taxa that are present in both datasets. Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies.ConclusionsThe phylogenetic analyses presented here represent the most comprehensive genome-level phylogenetic analyses in terms of taxa and data. Based on the availability of genome data for many bacterial species on GenBank, many other bacterial groups would also be amenable to similar genome-scale phylogenetic analyses even when present in multiple contigs. The result that collinear subsets of data are incongruent with the concatenated dataset and with each other while random data subsets show very little incongruence echoes the result of previous work on Shewanellaceae. The 44-taxon phylogenetic analysis presented here thus represents the future of phylogenomic analyses in scope and complexity.

Project description:BackgroundXanthomonas translucens pv. graminis (Xtg) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.ResultsIn this study, we produced high-quality, complete genome sequences of four strains of Xtg, complementing the recently obtained complete genome sequence of the Xtg pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related. A high number of transposases were exclusively found in Xtg and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of Xtg. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 plant cell wall degradative enzymes.ConclusionThese results suggest a high adaptability of Xtg, conferred by the abundance of mobile genetic elements, which could play a crucial role in pathogen adaptation. The large amount of such elements in Xtg compared to other pathovars of the species could, at least partially, explain its high virulence and broad host range. Conserved features that were specific to Xtg were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of Xtg.

Dataset Information

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

Publications

New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

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