scholarly journals Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

2021 ◽  
Author(s):  
Andreina I Castillo ◽  
Rodrigo P P Almeida
Keyword(s):  
Plant Pathogen ◽  
Geographic Origin ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Plant Host ◽  
Mixed Effect ◽  
Genomic Changes ◽  
Evolutionary Forces ◽  
Multiple Variables ◽  
Vector Borne

Abstract Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, Core vs. Accessory, and Recombinant vs. Non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs. natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.

Genomic Changes in Nucleotide and Dinucleotide Frequencies in Pasteurella multocida Cultured Under High Temperature

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1385-1394
Author(s):  
Xuhua Xia ◽  
Ting Wei ◽  
Zheng Xie ◽  
Antoine Danchin
Keyword(s):  
Vaccine Strain ◽  
Pasteurella Multocida ◽  
Virulent Strain ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Genomic Changes ◽  
Increasing Temperature ◽  
Cg Dinucleotides ◽  
Highly Virulent ◽  
Mutation And Selection

Abstract We used 94 RAPD primers of different nucleotide composition to probe the genomic differences between a highly virulent P. multocida strain and an attenuated vaccine strain derived from the virulent strain after culturing the latter under increasing temperature for ∼14,400 generations. The GC content of the vaccine strain is significantly (P < 0.05) lower than that of the virulent strain, contrary to the popular hypothesis of covariation between the GC content and temperature. The frequencies of AA, TA, and TT dinucleotides were higher, and those of AT, GC, and CG dinucleotides were lower, in the vaccine strain than in the virulent strain. A statistic called genomic RAPD entropy is formulated to measure the randomness of the genome, and the genome of the vaccine strain is more random than that of the virulent strain. These differences between the virulent and vaccine strains are interpreted in terms of mutation and selection under increased culturing temperature. A method for estimating substitution rates is developed in the appendix.

scholarly journals The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1805-1810 ◽  
Author(s):  
Martin J Lercher ◽  
Nick G C Smith ◽  
Adam Eyre-Walker ◽  
Laurence D Hurst
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Compositional Variation ◽  
Mutation Bias ◽  
Single Nucleotide ◽  
Frequency Distributions ◽  
Noncoding Regions ◽  
Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

2021 ◽  
Author(s):  
Neetu Tyagi ◽  
Rahila Sardar ◽  
Dinesh Gupta
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Respiratory Illness ◽  
Respiratory Viruses ◽  
Nucleotide Composition ◽  
Health Crisis ◽  
Study Results ◽  
Usage Patterns ◽  
The Difference

AbstractThe Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

scholarly journals Revisiting Orthotospovirus Phylogeny Using Whole Genomic Data and a Hypothesis for their Geographic Origin and Diversification

2020 ◽  
Author(s):  
Anamarija Butković ◽  
Rubén González ◽  
Santiago F. Elena
Keyword(s):  
Phylogenetic Relationships ◽  
Geographic Origin ◽  
Genome Shuffling ◽  
Genomic Data ◽  
Genomic Sequences ◽  
Genome Database ◽  
Evolutionary Forces ◽  
The Family ◽  
Plant Families ◽  
Negative Sense

ABSTRACTThe family Tospoviridae, a member of the Bunyavirales order, is constituted of tri-segmented negative-sense single-stranded RNA viruses that infect plants and are also able of replicating in their insect vectors in a persistent manner. The family is composed of a single genus, the Orthotospovirus, whose type species is Tomato spotted wilt virus (TSWV). Previous studies assessing the phylogenetic relationships within this genus were based upon partial genomic sequences, thus resulting in unresolved clades and a poor assessment of the roles of recombination and genome shuffling during mixed infections. Complete genomic data for most Orthotospovirus species are now available at NCBI genome database. In this study we have used 62 complete genomes from 20 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D), within the genus. We have estimated the split between the two major clades ∼3,100 years ago shortly followed by the split between the A and B phylogroups ∼2,860 years ago. The split between the C and D phylogroups happened more recently, ∼1,465 years ago. Segment reassortment has been shown to be important in the generation of novel viruses. Likewise, within-segment recombination events have been involved in the origin of new viral species. Finally, phylogeographic analyses of representative viruses suggests the Australasian ecozone as the possible origin of the genus, followed by complex patterns of migration, with rapid global spread and numerous reintroduction events.IMPORTANCEMembers of the Orthotospovirus genus infect a large number of plant families, including food crops and ornamentals, resulting in multimillionaire economical losses. Despite this importance, phylogenetic relationships within the genus were established years ago based in partial genomic sequences. A peculiarity of orthotospoviruses is their tri-segmented negative sense genomes, which makes segment reassortment and within-segment recombination, two forms of viral sex, potential evolutionary forces. Using full genomes from all described orthotospovirus species, we revisited their phylogeny and confirmed the existence of four major phylogroups with uneven geographic distribution. We have also shown a pervasive role of sex in the origin of new viral species. Finally, using Bayesian phylogeographic methods, we assessed the possible geographic origin and historical dispersal of representative viruses from the different phylogroups.

scholarly journals Evolution of Nucleotide Composition in the SARS-CoV-2 Lineage: Implications for Vaccine Design

2020 ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Base Composition ◽  
Scientific Community ◽  
Significant Positive Correlation ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Reverse Direction ◽  
Novel Coronavirus ◽  
Near Future ◽  
Systematic Reduction ◽  
Gc Contents

The worldwide outbreak of a novel coronavirus, SARS-CoV-2 has caused a pandemic of respiratory disease. Due to this emergency, researchers around the globe have been investigating the evolution of the genome of SARS-CoV-2 in order to design vaccines. Here I examined the evolution of GC content of SARS-CoV-2 by comparing the genomes of the members of the group Betacoronavirus. The results of this investigation revealed a highly significant positive correlation between the GC contents of betacoronaviruses and their divergence from SARS-CoV-2. The betacoronaviruses that are distantly related to SARS-CoV-2 have much higher GC contents than the latter. Conversely, the closely related ones have low GC contents, which are only slightly higher than that of SARS-CoV-2. This suggests a systematic reduction in the GC content in the SARS-CoV-2 lineage over time. The declining trend in this lineage predicts a much-reduced GC content in the coronaviruses that will descend/evolve from SARS-CoV-2 in the future. Due to the three consecutive outbreaks (MERS-CoV, SARS-CoV and SARS-CoV-2) caused by the members of the SARS-CoV-2, the scientific community is emphasizing the need for universal vaccines that are effective across many strains including those, that will inevitably emerge in the near future. The reduction in GC contents implies an increase in the rate of GC→AT mutations than that the mutational changes in the reverse direction. Therefore, understanding the evolution of base composition and mutational patterns of SARS-CoV-2 could be useful in designing broad-spectrum vaccines that could identify and neutralize the present and future strains of this virus.

scholarly journals Tri‐trophic interactions mediate the spread of a vector‐borne plant pathogen

Ecology ◽  
2019 ◽  
Vol 100 (11) ◽  
Author(s):  
Robert E. Clark ◽  
Saumik Basu ◽  
Benjamin W. Lee ◽  
David W. Crowder
Keyword(s):  
Trophic Interactions ◽  
Plant Pathogen ◽  
Vector Borne

scholarly journals Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

mBio ◽  
2013 ◽  
Vol 4 (3) ◽  
Author(s):  
Ousmane H. Cissé ◽  
João M. G. C. F. Almeida ◽  
Álvaro Fonseca ◽  
Ajay Anand Kumar ◽  
Jarkko Salojärvi ◽  
...  
Keyword(s):  
Plant Disease ◽  
Plant Cell Wall ◽  
Glyoxylate Cycle ◽  
Gc Content ◽  
Fruit Production ◽  
Infection Process ◽  
Detoxification Enzymes ◽  
Plant Host ◽  
Content Type ◽  
Leaf Curl

ABSTRACT Taphrina deformans is a fungus responsible for peach leaf curl, an important plant disease. It is phylogenetically assigned to the Taphrinomycotina subphylum, which includes the fission yeast and the mammalian pathogens of the genus Pneumocystis. We describe here the genome of T. deformans in the light of its dual plant-saprophytic/plant-parasitic lifestyle. The 13.3-Mb genome contains few identifiable repeated elements (ca. 1.5%) and a relatively high GC content (49.5%). A total of 5,735 protein-coding genes were identified, among which 83% share similarities with other fungi. Adaptation to the plant host seems reflected in the genome, since the genome carries genes involved in plant cell wall degradation (e.g., cellulases and cutinases), secondary metabolism, the hallmark glyoxylate cycle, detoxification, and sterol biosynthesis, as well as genes involved in the biosynthesis of plant hormones. Genes involved in lipid metabolism may play a role in its virulence. Several locus candidates for putative MAT cassettes and sex-related genes akin to those of Schizosaccharomyces pombe were identified. A mating-type-switching mechanism similar to that found in ascomycetous yeasts could be in effect. Taken together, the findings are consistent with the alternate saprophytic and parasitic-pathogenic lifestyles of T. deformans. IMPORTANCE Peach leaf curl is an important plant disease which causes significant losses of fruit production. We report here the genome sequence of the causative agent of the disease, the fungus Taphrina deformans. The genome carries characteristic genes that are important for the plant infection process. These include (i) proteases that allow degradation of the plant tissues; (ii) secondary metabolites which are products favoring interaction of the fungus with the environment, including the host; (iii) hormones that are responsible for the symptom of severely distorted leaves on the host; and (iv) drug detoxification enzymes that confer resistance to fungicides. The availability of the genome allows the design of new drug targets as well as the elaboration of specific management strategies to fight the disease.

scholarly journals Genetic and Virulence Variability Among Erwinia tracheiphila Strains Recovered from Different Cucurbit Hosts

2013 ◽  
Vol 103 (9) ◽  
pp. 900-905 ◽  
Author(s):  
E. Saalau Rojas ◽  
P. M. Dixon ◽  
J. C. Batzer ◽  
M. L. Gleason
Keyword(s):  
Cucumis Melo ◽  
Geographic Origin ◽  
Strain Specificity ◽  
Plant Host ◽  
Erwinia Tracheiphila ◽  
Host Genus ◽  
Summer Squash ◽  
The Family ◽  
Polymerase Chain ◽  
Cucurbit Bacterial Wilt

The causal agent of cucurbit bacterial wilt, Erwinia tracheiphila, has a wide host range in the family Cucurbitaceae, including economically important crops such as muskmelon (Cucumis melo), cucumber (C. sativus), and squash (Cucurbita spp.). Genetic variability of 69 E. tracheiphila strains was investigated by repetitive-element polymerase chain reaction (rep-PCR) using BOXA1R and ERIC1-2 primers. Fingerprint profiles revealed significant variability associated with crop host; strains isolated from Cucumis spp. were clearly distinguishable from Cucurbita spp.-isolated strains regardless of geographic origin. Twelve E. tracheiphila strains isolated from muskmelon, cucumber, or summer squash were inoculated onto muskmelon and summer squash seedlings, followed by incubation in a growth chamber. Wilt symptoms were assessed over 3 weeks, strains were reisolated, and rep-PCR profiles were compared with the inoculated strains. Wilting occurred significantly faster when seedlings were inoculated with strains that originated from the same crop host genus (P<0.001). In the first run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon seedlings at a median of 7.8 and 5.6 days after inoculation (dai), respectively. Summer squash seedlings wilted 18.0, 15.7, and 5.7 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. In a second run of the experiment, cucumber and muskmelon strains caused wilting on muskmelon at 7.0 and 6.9 dai, respectively, whereas summer squash seedlings wilted at 23.6, 29.0 and 9.0 dai when inoculated with muskmelon-, cucumber-, and squash-origin strains, respectively. Our results provide the first evidence of genetic diversity within E. tracheiphila and suggest that strain specificity is associated with plant host. This advance is a first step toward understanding the genetic and population structure of E. tracheiphila.

Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments

2012 ◽  
Vol 58 (6) ◽  
pp. 767-775 ◽  
Author(s):  
Ola A. Olapade ◽  
Kayleigh Pung
Keyword(s):  
Invasive Species ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Native Plants ◽  
Plant Host ◽  
Cedar Creek ◽  
Kalamazoo River ◽  
Multiple Variables ◽  
Freshwater Environments

Plant–microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple ( Podophyllum peltatum L.) and cow parsnip ( Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard ( Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

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