scholarly journals Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts

2013 ◽  
Vol 94 (2) ◽  
pp. 418-431 ◽  
Author(s):  
Alison T. M. Lima ◽  
Roberto R. Sobrinho ◽  
Jorge González-Aguilera ◽  
Carolina S. Rocha ◽  
Sarah J. C. Silva ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Nucleotide Substitution ◽  
Plant Viruses ◽  
Cultivated Plants ◽  
Spot Virus ◽  
Adaptive Selection ◽  
Site Variation ◽  
Cultivated Plant ◽  
Nucleotide Substitution Rates ◽  
Whitefly Vector

Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.

scholarly journals Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts

2014 ◽  
Vol 95 (11) ◽  
pp. 2540-2552 ◽  
Author(s):  
Roberto Ramos Sobrinho ◽  
César Augusto Diniz Xavier ◽  
Hermano Monteiro de Barros Pereira ◽  
Gaus Silvestre de Andrade Lima ◽  
Iraíldes Pereira Assunção ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
A Priori ◽  
Lima Bean ◽  
Plant Viruses ◽  
Phaseolus Lunatus ◽  
Cultivated Plants ◽  
A Genome ◽  
Host Effect ◽  
Macroptilium Lathyroides

Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels' where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography.

scholarly journals Tomato Spotted Wilt Tosporvirus and its Thrips Vectors: Epidemiology, Insect/Virus Interactions and Control

1999 ◽  
Author(s):  
Diane E. Ullman ◽  
Benjamin Raccah ◽  
John Sherwood ◽  
Meir Klein ◽  
Yehezkiel Antignus ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
Plant Viruses ◽  
Cultivated Plants ◽  
Virus Spread ◽  
Vector Species ◽  
Spot Virus ◽  
Tomato Spotted Wilt ◽  
Thrips Species ◽  
First Time

Objectives. The major aim of the proposed research was to study thrips-TSWV relationships and their role in the epidemiology of the virus with the aim of using this knowledge to reduce crop losses occurring due to epidemics. Our specific objectives were: To determine the major factors involved in virus outbreaks, including: a) identifying the thrips species involved in virus dissemination and their relative role in virus spread; b) determining the virus sources among wild and cultivated plants throughout the season and their role in virus spread, and, c) determining how temperature and molecular variations in isolates impact virus replication in plants and insects and impact the transmission cycle. Background to the topic. Tospoviruses are among the most important emerging plant viruses that impact production of agricultural and ornamental crops. Evolution of tospoviruses and their relationships with thrips vector species have been of great interest because of crop damage caused world wide and the complete absence of suitable methods of control. Tospoviruses threaten crops in Israel and the United States. By understanding the factors contributing to epidemics and the specific relationships between thrips species and particular tospoviruses we hope that new strategies for control can be developed that will benefit agriculture in both Israel and the United States. Major conclusions, solutions, achievements. We determined that at least three tospoviruses were involved in epidemics in Israel and the United States, tomato spotted wilt virus (TSWV), impatiens necrotic spot virus (INSV) and iris yellow spot virus (IYSV). We detected and characterized INSV for the first time in Israel and, through our efforts, IYSV was detected and characterized for the first time in both countries. We demonstrated that many thrips species were present in commercial production areas and trap color influenced thrips catch. Frankliniella occidentalis was the major vector species of INSV and TSWV and populations varied in transmission efficiency. Thrips tabaci is the sole known vector of IYSV and experiments in both countries indicated that F. occidentalis is not a vector of this new tospovirus. Alternate plant hosts were identified for each virus. A new monitoring system combining sticky cards and petunia indicator plants was developed to identify sources of infective thrips. This system has been highly successful in the U.S. and was used to demonstrate to growers that removal of plant sources of infective thrips has a dramatic impact on virus incidence. Finally, a putative thrips receptor mediating acquisition of TSWV was discovered. Implications, scientific and agricultural. Our findings have contributed to new control measures that will benefit agriculture. Identification of a putative thrips receptor for TSWV and our findings relative to thrips/tospovirus specificity have implications for development of innovative new control strategies.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

scholarly journals QUANTIFICATION OF MAJOR PHYTOCHEMICALS OF SWERTIA CHIRAYITA, A MEDICINAL PLANT FROM NEPAL

1970 ◽  
Vol 17 ◽  
pp. 59-68 ◽  
Author(s):  
Susanna Phoboo ◽  
Marcia Da Silva Pinto ◽  
Prasanta C. Bhowmik ◽  
Pramod Kumar Jha ◽  
Kalidas Shetty
Keyword(s):  
Medicinal Plant ◽  
High Performance ◽  
Cultivated Plants ◽  
Swertia Chirayita ◽  
Plant Parts ◽  
Central Nepal ◽  
Significant Difference ◽  
Cultivated Plant ◽  
Array Detection ◽  
Important Medicinal Plant

Swertia chirayita is an important medicinal plant from Nepal with anti-diabetic, anti-pyretic, anti-malarial and anti-inflammatory potential and used in therapeutic herbal preparations in parts of South Asia. The main phytochemicals in crude aqueous and ethanolic extracts of different plant parts of Swertia chirayita collected from nine different districts of Nepal representing West, East and Central Nepal were quantified using HPLC/DAD (High Performance Liquid Chromatography-Diode Array Detection). The quantities of these phytochemicals were also compared between wild and cultivated plant parts of Swertia chirayita. Amarogentin, mangiferin, swertiamarin were the main phytochemicals in all extracts. The highest quantity of all the three phytochemicals was found in IL (inflorescence and leaf mixture) of all the collected plants samples. There was no significant difference in the amounts of these three phytochemicals between extracts from wild and cultivated plants. The result from this study substantiates the validity of cultivated Swertia chirayita for medicinal purposes and trade.Key words:  Swertia chirayita; HPLC/DAD; Wild; Cultivated; Phytochemicals; Quantification; Mangiferin; Swertiamarin; AmarogentinDOI: 10.3126/eco.v17i0.4118EcoprintAn International Journal of EcologyVol. 17, 2010Page: 59-68Uploaded date: 3 January, 2011

scholarly journals PERANAN TUMBUHAN LIAR DALAM KONSERVASI SERANGGA PENYERBUK ORDO HYMENOPTERA

2016 ◽  
Vol 10 (2) ◽  
pp. 195
Author(s):  
Erniwati Erniwati ◽  
Sih Kahono
Keyword(s):  
Flowering Time ◽  
Food Resources ◽  
Wild Plants ◽  
Cultivated Plants ◽  
Applied Study ◽  
Insect Pollinators ◽  
Cultivated Plant ◽  
Dry Seasons

The role of the wild plants in relation to the conservation of the Indonesian insectpollinators was studied at several areas of Java. Three of direct observationmethods were applied: study of biodiversity and observation on the wild flowersand the insect pollinators as well, and the behaviour of the insects. The flowersof wild plants were relatively smaller and paler in colour, however they were moreattractive to insect pollinators than cultivated plants. Flowering time of the wildplants was mostly during wet seasons, contrary to that of the cultivated plantswhich was mostly during dry seasons. Our observation indicated that these wildplants are the food resources of insect pollinators during wet seasons. Observationdata support the importance of wild plants to supply food to insect pollinatorsduring wet seasons. Management of wild and cultivated plant environments isnecessary to conserve insect pollinators.

Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts

2019 ◽  
Vol 6 (1) ◽  
pp. 411-433 ◽  
Author(s):  
Fernando García-Arenal ◽  
Francisco Murilo Zerbini
Keyword(s):  
Genetic Variation ◽  
Ecological Factors ◽  
Plant Viruses ◽  
Crop Plants ◽  
Wild Plants ◽  
Wild Plant ◽  
Cultivated Plants ◽  
Emerging Pathogens ◽  
Epidemiological Features ◽  
Virus Emergence

Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses’ potential to emerge in crops.

scholarly journals Plant Virus Metagenomics: Advances in Virus Discovery

2015 ◽  
Vol 105 (6) ◽  
pp. 716-727 ◽  
Author(s):  
Marilyn J. Roossinck ◽  
Darren P. Martin ◽  
Philippe Roumagnac
Keyword(s):  
Nucleic Acids ◽  
Deep Sequencing ◽  
Plant Virus ◽  
Virus Disease ◽  
Plant Viruses ◽  
Wild Plants ◽  
Cultivated Plants ◽  
Virus Discovery ◽  
Virus Infections ◽  
Virus Like Particles

In recent years plant viruses have been detected from many environments, including domestic and wild plants and interfaces between these systems—aquatic sources, feces of various animals, and insects. A variety of methods have been employed to study plant virus biodiversity, including enrichment for virus-like particles or virus-specific RNA or DNA, or the extraction of total nucleic acids, followed by next-generation deep sequencing and bioinformatic analyses. All of the methods have some shortcomings, but taken together these studies reveal our surprising lack of knowledge about plant viruses and point to the need for more comprehensive studies. In addition, many new viruses have been discovered, with most virus infections in wild plants appearing asymptomatic, suggesting that virus disease may be a byproduct of domestication. For plant pathologists these studies are providing useful tools to detect viruses, and perhaps to predict future problems that could threaten cultivated plants.

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

2017 ◽  
Vol 84 (4) ◽  
pp. 187-203 ◽  
Author(s):  
Erika N. Schwarz ◽  
Tracey A. Ruhlman ◽  
Mao-Lun Weng ◽  
Mohammad A. Khiyami ◽  
Jamal S. M. Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Substitution Rates ◽  
Genome Features ◽  
Nucleotide Substitution Rates

scholarly journals Evolutionary Dynamics and Global Diversity of Influenza A Virus

2015 ◽  
Vol 89 (21) ◽  
pp. 10993-11001 ◽  
Author(s):  
Daniel Rejmanek ◽  
Parviez R. Hosseini ◽  
Jonna A. K. Mazet ◽  
Peter Daszak ◽  
Tracey Goldstein
Keyword(s):  
East Asia ◽  
Influenza A Virus ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitution ◽  
Health Care Spending ◽  
Asian Countries ◽  
Substitution Rates ◽  
Country Level ◽  
Nucleotide Substitution Rates

ABSTRACTThe increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin (e.g., H5N1 and H7N9) in recent years underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 to 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socioeconomic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly in East Asia, than in Canada and the United States. Similarly, at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America. In contrast, the selection pressures (measured as ratios of nonsynonymous to synonymous evolutionary changes [dN/dSratios]) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort (i.e., total number of strains reported) and health care spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including a lack of sequences submitted from large portions of Africa and South America and a lack of geolocation information) and in broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world.IMPORTANCEIn recent years, an increasing number of influenza A virus (IAV) subtypes, including H5N1, H7N9, and H10N8, have been detected in humans. High fatality rates have led to an increased urgency to better understand where and how novel pathogenic influenza virus strains emerge. Our findings showed that mutational rates of 11 commonly encountered subtypes were higher in East Asian countries than in North America, suggesting that there may be a greater risk for the emergence of novel pathogenic strains in East Asia. In assessing the potential drivers of IAV subtype diversity, our analyses confirmed that reporting effort and health care spending were the best predictors of the observed subtype diversity at the country level. These findings underscore the need to increase sampling and reporting efforts for all subtypes in many undersampled countries throughout the world.

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