The genomic diversification of grapevine clones.

BACKGROUND:Vegetatively propagated clones accumulate somatic mutations. The purpose of this study was to better appreciate clone diversity and involved defining the nature of somatic mutations throughout the genome. Fifteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. RESULTS:Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than in genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and because methylated cytosines often spontaneously deaminate. Of the minority of mutations that occurred in exons, larger proportions of these were putatively deleterious when they occurred in relatively few clones. CONCLUSIONS:These data support three major conclusions. First, repetitive intergenic space is a major driver of clone genome diversification. Second, clones accumulate putatively deleterious mutations. Third, the data suggest selection against deleterious variants in coding regions or some mechanism by which mutations are less frequent in coding than noncoding regions of the genome

Cfr(B), cfr(C), and a New cfr-Like Gene, cfr(E), in Clostridium difficile Strains Recovered across Latin America

Indexación: Scopus.Cfr is a radical S-adenosyl-L-methionine (SAM) enzyme that confers cross-resistance to antibiotics targeting the 23S rRNA through hypermethylation of nucleotide A2503. Three cfr-like genes implicated in antibiotic resistance have been described, two of which, cfr(B) and cfr(C), have been sporadically detected in Clostridium difficile. However, the methylase activity of Cfr(C) has not been confirmed. We found cfr(B), cfr(C), and a cfr-like gene that shows only 51 to 58% protein sequence identity to Cfr and Cfr-like enzymes in clinical C. difficile isolates recovered across nearly a decade in Mexico, Honduras, Costa Rica, and Chile. This new resistance gene was termed cfr(E). In agreement with the anticipated function of the cfrlike genes detected, all isolates exhibited high MIC values for several ribosome-targeting antibiotics. In addition, in vitro assays confirmed that Cfr(C) and Cfr(E) methylate Escherichia coli and, to a lesser extent, C. difficile 23S rRNA fragments at the expected positions. The analyzed isolates do not have mutations in 23S rRNA genes or genes encoding the ribosomal proteins L3 and L4 and lack poxtA, optrA, and pleuromutilin resistance genes. Moreover, these cfr-like genes were found in Tn6218-like transposons or integrative and conjugative elements (ICE) that could facilitate their transfer. These results indicate selection of potentially mobile cfr-like genes in C. difficile from Latin America and provide the first assessment of the methylation activity of Cfr(C) and Cfr(E), which belong to a cluster of Cfr-like proteins that does not include the functionally characterized enzymes Cfr, Cfr(B), and Cfr(D).https://journals.asm.org/doi/10.1128/AAC.01074-1

Genetic improvement of tomato by targeted control of fruit softening

Controlling the rate of softening to extend shelf life was a key target for researchers engineering genetically modified (GM) tomatoes in the 1990s, but only modest improvements were achieved. Hybrids grown nowadays contain 'non-ripening mutations' that slow ripening and improve shelf life, but adversely affect flavor and color. We report substantial, targeted control of tomato softening, without affecting other aspects of ripening, by silencing a gene encoding a pectate lyase

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

Histopathological Findings in Brain Tissue Obtained during Epilepsy Surgery

BACKGROUND: Detailed neuropathological information on the structural brain lesions underlying seizures is valuable for understanding drug-resistant focal epilepsy. / METHODS: We report the diagnoses made on the basis of resected brain specimens from 9523 patients who underwent epilepsy surgery for drug-resistant seizures in 36 centers from 12 European countries over 25 years. Histopathological diagnoses were determined through examination of the specimens in local hospitals (41%) or at the German Neuropathology Reference Center for Epilepsy Surgery (59%). / RESULTS: The onset of seizures occurred before 18 years of age in 75.9% of patients overall, and 72.5% of the patients underwent surgery as adults. The mean duration of epilepsy before surgical resection was 20.1 years among adults and 5.3 years among children. The temporal lobe was involved in 71.9% of operations. There were 36 histopathological diagnoses in seven major disease categories. The most common categories were hippocampal sclerosis, found in 36.4% of the patients (88.7% of cases were in adults), tumors (mainly ganglioglioma) in 23.6%, and malformations of cortical development in 19.8% (focal cortical dysplasia was the most common type, 52.7% of cases of which were in children). No histopathological diagnosis could be established for 7.7% of the patients. / CONCLUSIONS: In patients with drug-resistant focal epilepsy requiring surgery, hippocampal sclerosis was the most common histopathological diagnosis among adults, and focal cortical dysplasia was the most common diagnosis among children. Tumors were the second most common lesion in both groups. (Funded by the European Union and others.

RNA-seq analysis in plant–fungus interactions

Many fungi are pathogens that infect important food and plantation crops, reducing both yield and quality of food products. Understanding plant–fungus interactions is crucial as knowledge in this area is required to formulate sustainable strategies to improve plant health and crop productivity. High-throughput RNA-sequencing (RNA-seq) enables researchers to gain insights of the mixed and multispecies transcriptomes in plant–fungus interactions. Interpretation of huge data generated by RNA-seq has led to new insights in this area, facilitating a system approach in unraveling interactions between plant hosts and fungal pathogens. In this review, the application and challenges of RNA-seq analysis in plant–fungus interactions will be discussed

Abundance patterns (1984-1987 / 1994-1998) of polychaete worms (Annelida) from an estuarine tidal flat, Pacific, Costa Rica

The objectives of this report are to provide an updated list of the annelid polychaete worm species found at a tropical estuarine intertidal flat, describe long term oscillations of 11 of the species, and the impact of red tides as evidenced by PCA. From 1984 to 1987 (49 dates) 14 sediment cores (17.7 cm2 – 15 cm deep) were collected per date at low tide from a 400 m2 muddy-sand plot in the Gulf of Nicoya estuary (10o N-85o W), Pacific, Costa Rica. All cores were fixed in Rose Bengal stained formalin and sieved thru a 500 micron mesh screen. A total of 43 species of polychaetes were found and distributed among 25 families and 6600 individuals, of which 80% were represented by: Mediomastus californiensis (32.4%), Caraziella calafia (20.3%), Paraprionospio alata (9.2%), Scolotema tetraura (5.9%), Gymnonereis crosslandi (4.9%), Spiophanex duplex (3.8%), and Glycinde armigera (3.5%). M. californiensis was numerically dominant during most of the sampling dates. The Spionidae (6), Phyllodocidae (4), and Nereididae (3) were the more speciose polychaete families. Populations of all species were patchy in space and time. The abundance patterns of 11 species are illustrated for the 1984-1987 data set. These patterns may reflect declining populations at the beginning of 1984 perhaps influenced by the strong 1982-1983 ENSO event. During 1985 red tides may have influenced the abundances of polychaetes as indicated by the results of a PCA. This is the first time that population patterns of nine species of intertidal polychaetes over a three year period, and the impact of red tides on these worms are reported for this region of the eastern Pacific. General Additive Models (GAM) were applied to the abundances of M. californiensis and P. alata found during 1984-1987 and to additional data from 1994 to 1996 (28 dates) The GAM approach confirmed ealier observations of seasonal oscillations of these species during 1984- 1987, but these trends were not found during 1994-1998. Previously unnoticed underlying patterns of unknown origin were also detected by the application of GAM. The theoretical framework needed for the interpretation of results from tropical benthic surveys could improve significantly from more long term monitoring. Long term abundance data is essential to evaluate the impacts of anthropogenic activities in estuaries.Los objetivos de este estudio fueron el proveer una lista actualizada de las especies de gusanos anélidos poliquetos encontrados en una planicie tropical de entre-mareas, describir oscilaciones de largo plazo de 11 de esas especies y el impacto de mareas rojas evidenciadas por el análisis de PCA. Desde 1984 a 1987 (49 fechas) 14 núcleos de sedimento (17.7 cm2 –15 cm de profundidad) fueron colectados por fecha en marea baja en un sitio fangoso-arenoso de 400 m2 en el estuario del Golfo de Nicoya (10o N-85o W), Pacifico, Costa Rica. Todos los núcleos fueron fijados en formalina en agua de mar tenida con Rosa de Bengala y tamizados en una malla de 500 micras de poro. Se encontró un total de 43 especies de gusanos poliquetos distribuidos entre 25 familias y 6600 individuos, de los que un 80% estaban representados por: Mediomastus californiensis (32.4%), Caraziella calafia (20.3%), Paraprionospio alata (9.2%), Scolotema tetraura (5.9%), Gymnonereis crosslandi (4.9%), Spiophanex duplex (3.8%) y Glycinde armigera (3.5%). M. californiensis fue numéricamente dominante durante la mayoria de las fechas de muestreo. Las Spionidae (6), Phyllodocidae (4), y Nereididae (3) fueron las familias de poliquetos con más especies. Las poblaciones de todas las especies fueron irregulares en el tiempo y en el espacio. Se ilustran los patrones de abundancia de 11 de las especies para el periodo 1984-1987. Estos patrones pueden reflejar poblaciones en decadencia al inicio de 1984, tal vez influenciadas por el fuerte evento ENSO de 1982-1983. Durante 1985 las mareas rojas pueden haber influenciado las abundancias de poliquetos según lo indican los resultados de un PCA. Esta es la primera vez para el Pacífico del Este que se ilustran las oscilaciones poblacionales de nueve especies de poliquetos de entre mareas a lo largo de un período de tres años, así como el impacto de las mareas rojas en estos gusanos. Se aplicó el análisis por Modelos Aditivos Generales (GAM) a las abundancias de M. californiensis y P. alata recolectados durante 1984-1987 y adicionalmente entre 1994 y 1996 (28 fechas). El enfoque GAM confirmó las observaciones anteriores sobre la estacionalidad de estas especies durante 1984-1987, pero estas tendencias no fueron encontradas durante 1994-1998. Mediante el uso de GAM fueron también detectados patrones de origen desconocido no notados anteriormente. El marco teórico necesario para la interpretación de los resultados de estudios bénticos tropicales puede mejorarse mediante la realización de más monitoreos a largo plazo. Datos de abundancia de largo plazo son esenciales para evaluar los impactos de actividades antropogénicas en estuarios.Universidad de Costa Rica/[808-B3-113]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias del Mar y Limnología (CIMAR)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Sistema de Educación General::Escuela de Estudios GeneralesUCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí