scholarly journals Gene Duplication Is Infrequent in the Recent Evolutionary History of RNA Viruses

2013 ◽  
Vol 30 (6) ◽  
pp. 1263-1269 ◽  
Author(s):  
Etienne Simon-Loriere ◽  
Edward C. Holmes
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Rna Viruses ◽  
History Of

Systematic evidence from gene duplication and regulation

1990 ◽  
Vol 3 (1) ◽  
pp. 145
Author(s):  
DJ Colgan
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Tandem Duplication ◽  
Fragment Length Polymorphism ◽  
Duplicate Genes ◽  
Polymorphism Analysis ◽  
Multiple Origins ◽  
The Family ◽  
History Of ◽  
Phylogenetic Hypotheses

This paper is a review of the use of information regarding the presence of duplicate genes and their regulation in systematics. The review concentrates on data derived from protein electrophoresis and restriction fragment length polymorphism analysis. The appearance of a duplication in a subset of a group of species implies that the members of the subset belong to the same clade. Suppression of the duplication may render this clade apparently paraphyletic, but may itself be informative of relations within the lineage through patterns of loss of expression in all, or some tissues, or through restrictions of the formation of functional heteropolymers in polymeric enzymes. Examples are given of studies which have used such information to establish phylogenetic hypotheses at the family level, to identify an auto- or allo-polyploid origin of polyploid species and to determine whether there have been single or multiple origins of such species. The likelihood of homoplasy in the patterns of appearance and regulation of duplicates depends on the molecular basis of the duplication. In particular, the contrast between the expected consequences of tandem duplication and the expression of pseudogenes emphasises the value of determining the mechanism of the original duplication. Many instances of sporadic gene duplication are now known, and polyploidisation is a common event in the evolutionary history of both plants and animals. So the opportunities to discover duplicationrelated characters will arise in many systematic studies. A program is presented to increase the chances that such useful information will be recognisable during the studies.

scholarly journals Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors Culex pipiens and Culex torrentium in Northern Europe

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1033 ◽  
Author(s):  
Pettersson ◽  
Shi ◽  
Eden ◽  
Holmes ◽  
Hesson
Keyword(s):  
Culex Pipiens ◽  
Evolutionary History ◽  
Rna Viruses ◽  
Mosquito Species ◽  
Animal Health ◽  
Mosquito Vectors ◽  
South Central ◽  
Global Movement ◽  
History Of ◽  
Local Habitat

Mosquitoes harbor an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruses sampled from mosquitoes in northerly regions. Here, we compared the RNA virome of two common northern mosquito species, Culex pipiens and Culex torrentium, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we documented similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Many viruses were also related to those sampled on other continents, indicative of a widespread global movement and/or long host–virus co-evolution. Although the two mosquito species investigated have overlapping geographical distributions and share many viruses, several viruses were only found at a specific location at this scale of sampling, such that local habitat and geography may play an important role in shaping viral diversity in Culex mosquitoes.

scholarly journals Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Delong Meng ◽  
Xueduan Liu ◽  
Xing Li ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Resistance Genes ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Metal Resistance ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
History Of

ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

The evolutionary history of vertebrate RNA viruses

Nature ◽  
2018 ◽  
Vol 556 (7700) ◽  
pp. 197-202 ◽  
Author(s):  
Mang Shi ◽  
Xian-Dan Lin ◽  
Xiao Chen ◽  
Jun-Hua Tian ◽  
Liang-Jun Chen ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Rna Viruses ◽  
History Of

The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression

2007 ◽  
Vol 12 (8) ◽  
pp. 358-367 ◽  
Author(s):  
Douglas E. Soltis ◽  
Hong Ma ◽  
Michael W. Frohlich ◽  
Pamela S. Soltis ◽  
Victor A. Albert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Evolutionary History ◽  
History Of

scholarly journals Author Correction: The evolutionary history of vertebrate RNA viruses

Nature ◽  
2018 ◽  
Vol 561 (7722) ◽  
pp. E6-E6 ◽  
Author(s):  
Mang Shi ◽  
Xian-Dan Lin ◽  
Xiao Chen ◽  
Jun-Hua Tian ◽  
Liang-Jun Chen ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Rna Viruses ◽  
History Of

scholarly journals A Sister Lineage of Sampled Retroviruses Corroborates the Complex Evolution of Retroviruses

2020 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Evolutionary History ◽  
Rna Viruses ◽  
Phylogenetic Analyses ◽  
Ribonuclease H ◽  
Genome Architecture ◽  
Major Lineage ◽  
Wide Range ◽  
History Of ◽  
Negative Sense ◽  
Complex Evolutionary History

Abstract The origin and deep history of retroviruses remain mysterious and contentious, largely because the diversity of retroviruses is incompletely understood. Here, we report the discovery of lokiretroviruses, a novel major lineage of retroviruses, within the genomes of a wide range of vertebrates (at least 137 species), including lampreys, ray-finned fishes, lobe-finned fishes, amphibians, and reptiles. Lokiretroviruses share a similar genome architecture with known retroviruses, but display some unique features. Interestingly, lokiretrovirus Env proteins share detectable similarity with fusion glycoproteins of viruses within the Mononegavirales order, blurring the boundary between retroviruses and negative sense single-stranded RNA viruses. Phylogenetic analyses based on reverse transcriptase demonstrate that lokiretroviruses are sister to all the retroviruses sampled to date, providing a crucial nexus for studying the deep history of retroviruses. Comparing congruence between host and virus phylogenies suggests lokiretroviruses mainly underwent cross-species transmission. Moreover, we find that retroviruses replaced their ribonuclease H and integrase domains multiple times during their evolutionary course, revealing the importance of domain shuffling in the evolution of retroviruses. Overall, our findings greatly expand our views of the diversity of retroviruses, and provide novel insights into the origin and complex evolutionary history of retroviruses.

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