scholarly journals Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

2020 ◽  
Author(s):  
César A.D. Xavier ◽  
Márcio T. Godinho ◽  
Talita B. Mar ◽  
Camila G. Ferro ◽  
Osvaldo F.L. Sande ◽  
...  
Keyword(s):  
New World ◽  
Evolutionary Dynamics ◽  
Bipartite Begomoviruses ◽  
Evolutionary Analysis ◽  
Host Interactions ◽  
Coding Regions ◽  
Evolutionary Studies ◽  
Genetic Clusters ◽  
Complete Genome Analysis ◽  
Different Levels

ABSTRACTSeveral key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of bipartite genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. We performed a parallel evolutionary analysis of the DNA-A and DNA-B components of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analyzed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both components, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate components belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and components.

Evolutionary Dynamics of Viruses or Microbes, but Not Both

2016 ◽  
Author(s):  
Joshua S. Weitz
Keyword(s):  
Life History ◽  
Evolutionary Dynamics ◽  
Selective Pressure ◽  
Host Interactions ◽  
Intermediate Phenotypes ◽  
Strong Selective Pressure ◽  
Evolution Of Resistance ◽  
Resistance To Infection ◽  
Host Evolution ◽  
Different Levels

This chapter discusses the evolutionary dynamics of viruses. Preexisting variation in host phenotypes include variants with different levels of susceptibility to viruses, including complete resistance. Formative studies of the basis of the mutation rate relied upon virus–host interactions and the possibility of the evolution of resistance to infection. Viruses represent a strong selective pressure and can induce evolution among hosts. Host evolution, as induced by viruses, includes novel forms of ecological dynamics, including cryptic dynamics. Infection of hosts represents a strong selective pressure for viruses. Viruses that differ in their life history traits vary in their fitness and can invade and replace existing viral strains. The latent period represents a model trait for the further study of the evolution of intermediate phenotypes. Evolution among other traits is also possible, including who infects whom.

scholarly journals Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

2021 ◽  
Author(s):  
César A.D. Xavier ◽  
Márcio T. Godinho ◽  
Talita B. Mar ◽  
Camila G. Ferro ◽  
Osvaldo F.L. Sande ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
Bipartite Begomoviruses ◽  
Complete Genome Analysis

scholarly journals Evolutionary design of regulatory control. II. Robust error-correcting feedback increases genetic and phenotypic variability

2018 ◽  
Author(s):  
Steven A. Frank
Keyword(s):  
Genetic Variability ◽  
Control Theory ◽  
Evolutionary Dynamics ◽  
Phenotypic Variability ◽  
Regulatory Control ◽  
Strong Increase ◽  
Evolutionary Analysis ◽  
High Heritability ◽  
Robust Systems ◽  
Different Levels

As systems become more robust against perturbations, they can compensate for greater sloppiness in the performance of their components. That robust compensation reduces the force of natural selection on the system’s components, leading to component decay. The paradoxical coupling of robustness and decay predicts that robust systems evolve cheaper, lower performing components, which accumulate greater mutational genetic variability and which have greater phenotypic stochasticity in trait expression. Previous work noted the paradox of robustness. However, no general theory for the evolutionary dynamics of system robustness and component decay has been developed. This article takes a first step by linking engineering control theory with the genetic theory of evolutionary dynamics. Control theory emphasizes error-correcting feedback as the single greatest principle in robust system design. Linking control theory to evolution leads to a theory for the evolutionary dynamics of error-correcting feedback, a unifying approach for the evolutionary analysis of robust systems. In this article, I study how, in theory, increasingly robust systems accumulate more genetic variability and greater stochasticity of expression in their components. The theory predicts different levels of variability between different regulatory control architectures and different levels of variability between different components within a particular regulatory control system. Those predictions provide a way to understand the accumulating data on genetic variability and single-cell stochasticity of gene expression. I also show that increasing robustness reduces the frequency of system failures associated with disease and, simultaneously, causes a strong increase in the heritability of disease. Thus, robust error correction in biological regulatory control may partly explain the puzzlingly high heritability of disease and, more generally, the surprisingly high heritability of fitness.

A test for rate‐coupling of trophic and cranial evolutionary dynamics in New World bats

Evolution ◽  
2021 ◽  
Author(s):  
Jeff J. Shi ◽  
Erin P. Westeen ◽  
Daniel L. Rabosky
Keyword(s):  
New World ◽  
Evolutionary Dynamics

scholarly journals Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Timothy D. Read ◽  
Sandeep J. Joseph ◽  
Xavier Didelot ◽  
Brooke Liang ◽  
Lisa Patel ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
New World ◽  
Evolutionary Dynamics ◽  
Chlamydia Psittaci ◽  
South American ◽  
Content Type ◽  
Sexually Transmitted ◽  
Genome Wide ◽  
Life Threatening ◽  
History Of

ABSTRACT Chlamydia psittaci is an obligate intracellular bacterium. Interest in Chlamydia stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans. C. psittaci human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen Chlamydia trachomatis. We sought to determine if similar evolutionary dynamics occurred in C. psittaci. We analyzed 20 C. psittaci genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that C. psittaci has a history of frequently switching hosts and undergoing recombination more often than C. trachomatis. Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced C. psittaci lineages or other Chlamydiaceae species. Three ancestral populations of C. psittaci were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. IMPORTANCE Chlamydia psittaci is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen Chlamydia trachomatis, we sought to determine if similar evolutionary dynamics occur in C. psittaci. Twenty C. psittaci genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for C. trachomatis. Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that C. psittaci strains have a history of frequently switching hosts and undergoing recombination.

scholarly journals Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 327 ◽  
Author(s):  
Gustavo Romay ◽  
Francis Geraud-Pouey ◽  
Dorys Chirinos ◽  
Mathieu Mahillon ◽  
Annika Gillis ◽  
...  
Keyword(s):  
Crop Production ◽  
New World ◽  
Systemic Infection ◽  
Plant Viruses ◽  
Monopartite Begomoviruses ◽  
Bipartite Begomoviruses ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Infectious Clones ◽  
Leaf Virus

Begomoviruses are one of the major groups of plant viruses with an important economic impact on crop production in tropical and subtropical regions. The global spread of its polyphagous vector, the whitefly Bemisia tabaci, has contributed to the emergence and diversification of species within this genus. In this study, we found a putative novel begomovirus infecting tomato plants in Venezuela without a cognate DNA-B component. This begomovirus was genetically characterized and compared with related species. Furthermore, its infectivity was demonstrated by agroinoculation of infectious clones in tomato (Solanum lycopersicum) and Nicotiana benthamiana plants. The name Tomato twisted leaf virus (ToTLV) is proposed. ToTLV showed the typical genome organization of the DNA-A component of New World bipartite begomoviruses. However, the single DNA component of ToTLV was able to develop systemic infection in tomato and N. benthamiana plants, suggesting a monopartite nature of its genome. Interestingly, an additional open reading frame ORF was observed in ToTLV encompassing the intergenic region and the coat protein gene, which is not present in other closely related begomoviruses. A putative transcript from this region was amplified by strand-specific reverse transcription-PCR. Along with recent studies, our results showed that the diversity of monopartite begomoviruses from the New World is greater than previously thought.

scholarly journals Variation in both host defense and prior herbivory can alter plant-vector-virus interactions

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xiaobin Shi ◽  
Evan L. Preisser ◽  
Baiming Liu ◽  
Huipeng Pan ◽  
Min Xiang ◽  
...  
Keyword(s):  
Plant Defense ◽  
Plant Virus ◽  
Major Focus ◽  
Host Interactions ◽  
Pest Detection ◽  
Virus Interactions ◽  
Leaf Curl Virus ◽  
Lower Plant ◽  
Different Levels ◽  
Whitefly Vector

Abstract Background While virus-vector-host interactions have been a major focus of both basic and applied ecological research, little is known about how different levels of plant defense interact with prior herbivory to affect these relationships. We used genetically-modified strains of tomato (Solanum lycopersicum) varying in the jasmonic acid (JA) plant defense pathways to explore how plant defense and prior herbivory affects a plant virus (tomato yellow leaf curl virus, ‘TYLCV’), its vector (the whitefly Bemisia tabaci MED), and the host. Results Virus-free MED preferred low-JA over high-JA plants and had lower fitness on high-JA plants. Viruliferous MED preferred low-JA plants but their survival was unaffected by JA levels. While virus-free MED did not lower plant JA levels, viruliferous MED decreased both JA levels and the expression of JA-related genes. Infestation by viruliferous MED reduced plant JA levels. In preference tests, neither virus-free nor viruliferous MED discriminated among JA-varying plants previously exposed to virus-free MED. However, both virus-free and viruliferous MED preferred low-JA plant genotypes when choosing between plants that had both been previously exposed to viruliferous MED. The enhanced preference for low-JA genotypes appears linked to the volatile compound neophytadiene, which was found only in whitefly-infested plants and at concentrations inversely related to plant JA levels. Conclusions Our findings illustrate how plant defense can interact with prior herbivory to affect both a plant virus and its whitefly vector, and confirm the induction of neophytadiene by MED. The apparent attraction of MED to neophytadiene may prove useful in pest detection and management.

Genomic diversity in the Leishmania donovani complex

Parasitology ◽  
1999 ◽  
Vol 119 (3) ◽  
pp. 237-246 ◽  
Author(s):  
I. L. MAURICIO ◽  
M. K. HOWARD ◽  
J. R. STOTHARD ◽  
M. A. MILES
Keyword(s):  
New World ◽  
Leishmania Donovani ◽  
Single Gene ◽  
Genomic Diversity ◽  
Leishmania Chagasi ◽  
Old World ◽  
Partial Sequencing ◽  
Random Amplification ◽  
Major Surface ◽  
Different Levels

The Leishmania donovani complex is considered to be composed of 3 species; L. donovani, L. infantum and L. chagasi, although this classification has been challenged. Genotypic relationships within the complex were evaluated at different levels by: binding of the probe Lmet9, specific for L. chagasi and Old World Leishmania spp.; partial sequencing of a constitutive major surface protease single gene (mspC) and random amplification of polymorphic DNA (RAPD). The Old World Leishmania spp. and the L. donovani complex have a monophyletic origin. Leishmania chagasi clearly belongs to the L. donovani complex but it is indistinguishable from L. infantum, which suggests introduction of L. chagasi into the New World in recent history. Leishmania infantum/L. chagasi was identified as a monophyletic group within the L. donovani complex but L. donovani may be paraphyletic. Diversity within L. donovani is substantial and phylogeographical patterns of association were found.

scholarly journals Evolution of the Mycobacterial SigK Regulon

2008 ◽  
Vol 190 (6) ◽  
pp. 1891-1899 ◽  
Author(s):  
Frédéric Veyrier ◽  
Battouli Saïd-Salim ◽  
Marcel A. Behr
Keyword(s):  
Sigma Factor ◽  
Regulatory System ◽  
Negative Regulator ◽  
Evolutionary Analysis ◽  
Regulatory Activity ◽  
Negative Regulators ◽  
Northern Blots ◽  
Antigenic Proteins ◽  
Evolutionary Studies ◽  
Variable Production

ABSTRACT Previous studies have established that members of the Mycobacterium tuberculosis complex exhibit variable production of the antigenic proteins MPT70 and MPT83 due to mutations in their positive regulator, SigK (sigma factor K), and their negative regulator, RskA (regulator of sigma K). To further understand this highly specific SigK-controlled regulon, we have undertaken evolutionary studies to determine the presence of homologues of SigK-regulated genes in other organisms and to predict its transcriptional network. Evolutionary analysis indicates that the positive and negative regulators are conserved across many organisms, but that the genes under their control are variable. Moreover, the addition, loss, and movement of various genes in the mpt70/83 locus suggest that these genes are unlikely to be cotranscribed. To test predictions from sequence analysis, we have used promoter luciferase fusions and Northern blots to show that the majority of genes in this locus have their own promoters, of which a subset are SigK regulated (mpt83, dipZ, mpt70, and Rv0449c). Next, we have shown that the intracellular inducibility of mpt70 and mpt83 is a conserved property, shared between M. tuberculosis and Mycobacterium marinum. In addition, we have shown that SigK and RskA from an environmental mycobacterium isolate (M. gilvum PYR-GCK) complemented the regulatory activity of M. tuberculosis ΔsigK rskA. Together, our data indicate that the regulatory system SigK/RskA is conserved across the Mycobacterium genus, whereas the regulon under its control varies considerably across species.

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