scholarly journals Insertion Sequence Diversity in Archaea

2007 ◽  
Vol 71 (1) ◽  
pp. 121-157 ◽  
Author(s):  
J. Filée ◽  
P. Siguier ◽  
M. Chandler
Keyword(s):  
Evolutionary History ◽  
Insertion Sequence ◽  
Prokaryotic Genome ◽  
Methanogenic Archaea ◽  
Insertion Sequences ◽  
Genome Sequences ◽  
The Public ◽  
Extensive Analysis ◽  
History Of ◽  
Families First

SUMMARY Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr ), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea.

scholarly journals Evidence of ancient papillomavirus recombination

2006 ◽  
Vol 87 (9) ◽  
pp. 2527-2531 ◽  
Author(s):  
Arvind Varsani ◽  
Eric van der Walt ◽  
Livio Heath ◽  
Edward P. Rybicki ◽  
Anna Lise Williamson ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Papillomavirus ◽  
Evolutionary History ◽  
Full Genome ◽  
Genome Sequences ◽  
Aids Epidemic ◽  
Immunodeficiency Virus ◽  
History Of ◽  
Hpv Types ◽  
Open Question

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties. Here, a range of rigorous analyses is applied to full-genome sequences of papillomaviruses to provide convincing statistical and phylogenetic evidence that evolutionarily relevant papillomavirus recombination can occur.

scholarly journals Metabolomic Insights into Marine Phytoplankton Diversity

Marine Drugs ◽  
2020 ◽  
Vol 18 (2) ◽  
pp. 78 ◽  
Author(s):  
Rémy Marcellin-Gros ◽  
Gwenaël Piganeau ◽  
Didier Stien
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Evolutionary History ◽  
Marine Phytoplankton ◽  
Genome Sequences ◽  
Phytoplankton Diversity ◽  
Sequencing Technologies ◽  
Unknown Species ◽  
History Of ◽  
Metabolomic Approach

The democratization of sequencing technologies fostered a leap in our knowledge of the diversity of marine phytoplanktonic microalgae, revealing many previously unknown species and lineages. The evolutionary history of the diversification of microalgae can be inferred from the analysis of their genome sequences. However, the link between the DNA sequence and the associated phenotype is notoriously difficult to assess, all the more so for marine phytoplanktonic microalgae for which the lab culture and, thus, biological experimentation is very tedious. Here, we explore the potential of a high-throughput untargeted metabolomic approach to explore the phenotypic–genotypic gap in 12 marine microalgae encompassing 1.2 billion years of evolution. We identified species- and lineage-specific metabolites. We also provide evidence of a very good correlation between the molecular divergence, inferred from the DNA sequences, and the metabolomic divergence, inferred from the complete metabolomic profiles. These results provide novel insights into the potential of chemotaxonomy in marine phytoplankton and support the hypothesis of a metabolomic clock, suggesting that DNA and metabolomic profiles co-evolve.

scholarly journals An African origin for Mycobacterium bovis

2020 ◽  
Vol 2020 (1) ◽  
pp. 49-59 ◽  
Author(s):  
Chloé Loiseau ◽  
Fabrizio Menardo ◽  
Abraham Aseffa ◽  
Elena Hailu ◽  
Balako Gumi ◽  
...  
Keyword(s):  
Population Structure ◽  
West Africa ◽  
Mycobacterium Bovis ◽  
Evolutionary History ◽  
Whole Genome ◽  
Genome Sequences ◽  
The World ◽  
History Of ◽  
Global Population ◽  
Different Parts

Abstract Background and objectives Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. Methodology We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. Results Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. Conclusions and implications Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. Lay summary During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.

scholarly journals Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hao Chung The ◽  
Ladaporn Bodhidatta ◽  
Duy Thanh Pham ◽  
Carl J. Mason ◽  
Tuyen Ha Thanh ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Disease Surveillance ◽  
Evolutionary History ◽  
Shigella Flexneri ◽  
Asian Countries ◽  
Genome Sequences ◽  
Evolutionary Trajectory ◽  
History Of ◽  
Susceptibility Patterns ◽  
Clonal Replacement

AbstractConventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s–1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.

Higher‐level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences

2019 ◽  
Vol 44 (4) ◽  
pp. 810-819 ◽  
Author(s):  
Yingqi Liu ◽  
Hu Li ◽  
Fan Song ◽  
Yisheng Zhao ◽  
John‐James Wilson ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Evolutionary History ◽  
Genome Sequences ◽  
History Of

scholarly journals Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽  
2010 ◽  
Vol 138 (13) ◽  
pp. 1737-1749 ◽  
Author(s):  
JOANA C. SILVA ◽  
AMY EGAN ◽  
ROBERT FRIEDMAN ◽  
JAMES B. MUNRO ◽  
JANE M. CARLTON ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Orthologous Gene ◽  
The Other ◽  
Divergence Times ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Malaria Parasites ◽  
Human Malaria ◽  
History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

scholarly journals Genome Sequences of a Rat Polyomavirus Related to Murine Polyomavirus, Rattus norvegicus Polyomavirus 1

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Bernhard Ehlers ◽  
Dania Richter ◽  
Franz-Rainer Matuschka ◽  
Rainer G. Ulrich
Keyword(s):  
Rattus Norvegicus ◽  
Evolutionary History ◽  
Genome Sequences ◽  
Breeding Colony ◽  
Complete Genomes ◽  
Hamster Polyomavirus ◽  
History Of ◽  
Murine Polyomavirus ◽  
Norway Rats

We amplified and sequenced six complete genomes of a polyomavirus from feral Norway rats ( Rattus norvegicus ) and from a long-term breeding colony derived from Norway rats. This virus, which is closely related to hamster polyomavirus and murine polyomavirus, may contribute to understanding the evolutionary history of rodent polyomaviruses.

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