scholarly journals Adaptive evolution ofMoniliophthoraPR-1 proteins towards its pathogenic lifestyle

2021 ◽  
Author(s):  
Adrielle A. Vasconcelos ◽  
Juliana José ◽  
Paulo M. Tokimatu Filho ◽  
Antonio P. Camargo ◽  
Paulo J. P. L. Teixeira ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Positive Selection ◽  
Adaptive Evolution ◽  
Theobroma Cacao ◽  
Main Function ◽  
Moniliophthora Perniciosa ◽  
Induced Expression ◽  
Pathogenesis Related ◽  
Parasitic Lifestyle ◽  
Moniliophthora Roreri

AbstractMoniliophthora perniciosaandMoniliophthora roreriare hemibiotrophic fungi that harbor a large number of Pathogenesis-Related 1 genes, many of which are induced in the biotrophic interaction withTheobroma cacao.Here, we provide evidence that the evolution of PR-1 inMoniliophthorawas adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Phylogenetic analysis revealed conserved PR-1 genes, shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity inMoniliophthora, as well as in recent specialization cases within both species. PR-1 families inMoniliophthorawith higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host-pathogen arm race. Furthermore, we show that the highly diversifiedMpPR-1genes are not induced by two phytoalexins, suggesting detoxification might not be their main function as proposed before.

scholarly journals Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Adrielle A. Vasconcelos ◽  
Juliana José ◽  
Paulo M. Tokimatu ◽  
Antonio P. Camargo ◽  
Paulo J. P. L. Teixeira ◽  
...  
Keyword(s):  
Positive Selection ◽  
Induced Defense ◽  
Phylogenetic Reconstruction ◽  
Main Function ◽  
Moniliophthora Perniciosa ◽  
Pathogenesis Related ◽  
Parasitic Lifestyle ◽  
Broom Disease ◽  
Plant Pathogenesis ◽  
Moniliophthora Roreri

Abstract Background Plant pathogenesis related-1 (PR-1) proteins belong to the CAP superfamily and have been characterized as markers of induced defense against pathogens. Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic fungi that respectively cause the witches’ broom disease and frosty pod rot in Theobroma cacao. Interestingly, a large number of plant PR-1-like genes are present in the genomes of both species and many are up-regulated during the biotrophic interaction. In this study, we investigated the evolution of PR-1 proteins from 22 genomes of Moniliophthora isolates and 16 other Agaricales species, performing genomic investigation, phylogenetic reconstruction, positive selection search and gene expression analysis. Results Phylogenetic analysis revealed conserved PR-1 genes (PR-1a, b, d, j), shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity in Moniliophthora (PR-1f, g, h, i), as well as in recent specialization cases within M. perniciosa biotypes (PR-1c, k, l) and M. roreri (PR-1n). PR-1 families in Moniliophthora with higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host–pathogen arms race. Furthermore, although previous work showed that MpPR-1 can detoxify plant antifungal compounds in yeast, we found that in the presence of eugenol M. perniciosa differentially expresses only MpPR-1e, k, d, of which two are not linked to pathogenicity, suggesting that detoxification might not be the main function of most MpPR-1. Conclusions Based on analyses of genomic and expression data, we provided evidence that the evolution of PR-1 in Moniliophthora was adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Additionally, we also discuss how fungal PR-1 proteins could have adapted from basal conserved functions to possible roles in fungal pathogenesis.

scholarly journals Caracterización de un jardín clonal de cacao (Theobroma cacao L.) en la amazonía peruana

2021 ◽  
Vol 1 (4) ◽  
pp. 30
Author(s):  
Máximo Parco ◽  
Alina A. Camacho ◽  
Jhimy A. Parco ◽  
Fiorela E. Dionisio
Keyword(s):  
Theobroma Cacao ◽  
Phytophthora Palmivora ◽  
Moniliophthora Perniciosa ◽  
Moniliophthora Roreri ◽  
Theobroma Cacao L

La variabilidad genética de clones de cacao (<em>Theobroma cacao</em> L.), que existe en el jardín clonal de la Estación Experimental Pichanaqui, de procedencia nacional e internacional, plantea la necesidad de realizar una caracterización morfológica a nivel de frutos, con descriptores morfológicos y escalas para cada tipo de tejido colectado, que usaron como auxiliares las siglas, los colores y formas que permitieron diferenciar las características de cada individuo. Las variables evaluadas fueron número de frutos por planta, peso de mazorcas maduras, numero de granos por mazorca, peso de almendras seca por mazorca, peso de 10 semillas secas, presencia de plagas como la Moniliasis (<em>Moniliophthora roreri</em>), Escoba de bruja (<em>Moniliophthora perniciosa</em>), Mancha parda (<em>Phytophthora palmivora</em>), Perforador (<em>Carmenta foraseminis</em>), Chinche amarillo (<em>Monalonium dissimulatum</em>) y calidad organoléptica en pulpa fresca. Además, se evaluaron variables económicas como el ingreso neto del clon por hectárea. Los resultados indicaron que los mejores clones por su productividad, tolerancia media a plagas y enfermedades, rentabilidad y sabor fueron: ICS 1, ICS 60, SCA 6, ICS 39, y TSH 565. En conclusión, se debería fomentar la siembra de estos clones en los productores de la zona a fin de mejorar su competitividad en el mercado local y nacional.

scholarly journals Adaptive Evolution of Feline Coronavirus Genes Based on Selection Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Hongyue Xia ◽  
Xibao Li ◽  
Wenliang Zhao ◽  
Shuran Jia ◽  
Xiaoqing Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Positive Selection ◽  
Adaptive Evolution ◽  
Mainland China ◽  
Virulence Proteins ◽  
Bayesian Phylogenetic Analysis ◽  
Genes Encoding ◽  
Severe Pathology ◽  
Virus Survival ◽  
Feline Coronavirus

Purpose. We investigated sequences of the feline coronaviruses (FCoV), which include feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV), from China and other countries to gain insight into the adaptive evolution of this virus. Methods. Ascites samples from 31 cats with suspected FIP and feces samples from 8 healthy cats were screened for the presence of FCoV. Partial viral genome sequences, including parts of the nsp12-nsp14, S, N, and 7b genes, were obtained and aligned with additional sequences obtained from the GenBank database. Bayesian phylogenetic analysis was conducted, and the possibility of recombination within these sequences was assessed. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Datamonkey platforms. Results. Of the 31 cats investigated, two suspected FIP cats and one healthy cat tested positive for FCoV. Phylogenetic analysis showed that all of the sequences from mainland China cluster together with a few sequences from the Netherlands as a distinct clade when analyzed with FCoV sequences from other countries. Fewer than 3 recombination breakpoints were detected in the nsp12-nsp14, S, N, and 7b genes, suggesting that analyses for positive selection could be conducted. A total of 4, 12, 4, and 4 positively selected sites were detected in the nsp12-nsp14, S, N, and 7b genes, respectively, with the previously described site 245 of the S gene, which distinguishes FIPV from FECV, being a positive selection site. Conversely, 106, 168, 25, and 17 negative selection sites in the nsp12-14, S, N, and 7b genes, respectively, were identified. Conclusion. Our study provides evidence that the FCoV genes encoding replicative, entry, and virulence proteins potentially experienced adaptive evolution. A greater number of sites in each gene experienced negative rather than positive selection, which suggests that most of the protein sequence must be conservatively maintained for virus survival. A few of the sites showing evidence of positive selection might be associated with the more severe pathology of FIPV or help these viruses survive other harmful conditions.

scholarly journals Proteomic response of Moniliophthora perniciosa exposed to pathogenesis-related protein-10 from Theobroma cacao

2013 ◽  
Vol 12 (4) ◽  
pp. 4855-4868 ◽  
Author(s):  
F.A.C. Silva ◽  
C.P. Pirovani ◽  
S. Menezes ◽  
C. Pungartnik ◽  
A.S. Santiago ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Related Protein ◽  
Moniliophthora Perniciosa ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related ◽  
Proteomic Response

scholarly journals Estrategias de control de Moniliophthora roreri y Moniliophthora perniciosa en Theobroma cacao L.: revisión sistemática

2016 ◽  
Vol 17 (3) ◽  
pp. 417 ◽  
Author(s):  
Paola Andrea Tirado-Gallego ◽  
Andrea Lopera-Álvarez ◽  
Leonardo Alberto Ríos-Osorio
Keyword(s):  
Costa Rica ◽  
Theobroma Cacao ◽  
Bacillus Sp ◽  
Moniliophthora Perniciosa ◽  
Trichoderma Sp ◽  
Revisión Sistemática ◽  
Moniliophthora Roreri ◽  
Theobroma Cacao L

<p>Una de las limitaciones más importantes de la producción de cacao (Theobroma cacao L.) a nivel mundial es la presencia de enfermedades causadas principalmente por hongos fitopatógenos del género Moniliophthora sp., especialmente, Moniliophthora roreri y Moniliophthora perniciosa, causantes de las enfermedades moniliasis y escoba de bruja, respectivamente. Ambas enfermedades son altamente invasivas y endémicas del cacao. El objetivo de este estudio fue describir las estrategias de control implementadas para manejar dichas enfermedades. Este sondeo se llevó a cabo en conformidad con la declaración Prisma (ítems de información con mayor reconocimiento para las revisiones sistemáticas y los metaanálisis), con base en una búsqueda sistemática de literatura en las bases de datos ScienceDirect, Springer Link y Scopus. Se incluyeron artículos originales de investigación reportados en la literatura científica en los últimos 12 años y se aplicaron criterios de inclusión y exclusión. Se encontró que el año en que más artículos se reportaron sobre el tema fue el 2008, en países como Brasil y Costa Rica. Las estrategias más utilizadas para el control de estas enfermedades son la remoción de mazorcas con signos de enfermedad, el empleo de fungidas a base de cobre y los controladores biológicos como Trichoderma sp. y Bacillus sp. Una de las metodologías más recomendadas es la optimización de los tratamientos mediante la combinación de agentes químicos, físicos y biológicos.</p>

POTENCIAL SANITARIO Y PRODUCTIVO DE 12 CLONES DE CACAO EN ECUADOR

2015 ◽  
Vol 38 (3) ◽  
pp. 265
Author(s):  
Fernando D. Sánchez-Mora ◽  
S. Mariela Medina-Jara ◽  
Gorki T. Díaz-Coronel ◽  
Rommel A. Ramos-Remache ◽  
Jaime F. Vera-Chang ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Moniliophthora Perniciosa ◽  
Moniliophthora Roreri ◽  
Theobroma Cacao L

El cacao (Theobroma cacao L.) es uno de los principales cultivos de importancia económica en el Ecuador, principalmente para los pequeños y medianos agricultores del litoral. Sin embargo, las enfermedades fungosas reducen el rendimiento de este cultivo. Durante los años 2008 a 2011 se evaluó en las localidades Quevedo y Tenguel, el comportamiento de 10 clones experimentales de cacao tipo Nacional con el objetivo de seleccionar los de mayor productividad y tolerancia a dos enfermedades: moniliasis (Moniliophthora roreri) y escoba de bruja (Moniliophthora perniciosa), en comparación con dos testigos comerciales (EET-103 y CCN-51). El diseño experimental fue de bloques completos al azar con arreglos factorial, con cuatro repeticiones. Se registró el número de escobas de bruja vegetativas, porcentaje de mazorcas enfermas, número de mazorcas sanas y totales, así como el rendimiento de almendras secas de cacao. El clon comercial CCN-51 presentó la menor incidencia de enfermedades, así como la mayor producción de mazorcas sanas y rendimiento promedio de almendras (1047.7 kg ha-1). Cuatro clones experimentales presentaron características deseables: L46-H57 con una mayor producción de mazorcas sanas y totales, L21-H43, L46-H57 y L46-H88 con un rendimiento de almendras superior a 550 kg ha-1, L18-H58 con el menor número de escoba de bruja (7.3), y L21-H43 con la menor incidencia de mazorcas enfermas (37.0 %). Estos clones pueden ser utilizados en programas de mejoramiento y conservación. La incidencia de enfermedades fúngicas y el rendimiento de almendras secas de cacao fueron mayores en Quevedo que en Tenguel.

scholarly journals The pathogenesis-related protein PR-4b from Theobroma cacao presents RNase activity, Ca2+ and Mg2+ dependent-DNase activity and antifungal action on Moniliophthora perniciosa

2014 ◽  
Vol 14 (1) ◽  
pp. 161 ◽  
Author(s):  
Sara Pereira Menezes ◽  
Edson de Andrade Silva ◽  
Eline Matos Lima ◽  
Aurizângela Oliveira de Sousa ◽  
Bruno Silva Andrade ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Rnase Activity ◽  
Dnase Activity ◽  
Related Protein ◽  
Moniliophthora Perniciosa ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related ◽  
Antifungal Action

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega &gt; 1$. As it is becoming increasingly clear that $\omega &gt; 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

Novel sources of witches’ broom resistance (causal agent Moniliophthora perniciosa) from natural populations of Theobroma cacao from the Brazilian Amazon

Euphytica ◽  
2009 ◽  
Vol 172 (1) ◽  
pp. 125-138 ◽  
Author(s):  
Paulo S. B. de Albuquerque ◽  
Stela D. V. M. Silva ◽  
Edna D. M. N. Luz ◽  
José L. Pires ◽  
Afrânio M. C. Vieira ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Natural Populations ◽  
Brazilian Amazon ◽  
Causal Agent ◽  
Moniliophthora Perniciosa

scholarly journals The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Li ◽  
Yunyun Lv ◽  
Zhengyong Wen ◽  
Chao Bian ◽  
Xinhui Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Physiological Activity ◽  
Complete Mitochondrial Genome ◽  
Dynamic Environment ◽  
Data Set ◽  
History Of ◽  
Complete Mitogenome ◽  
Selection Signal ◽  
Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

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