Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid.

BACKGROUND:Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava's responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. RESULTS:The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. CONCLUSIONS:This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA

Análisis proteómico de células de Hepatoma Huh7 transfectadas con MAT1A.Caracterización de DDX3X como diana de la S-adenosilmetionina

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Patagonotothen tessellata

This demersal species inhabits nearshore rocky reefs and kelp forests in southern Chile and Argentina and has an estimated generation length of 5 years. The global-level center of its abundance is in the straits of southern Chile. Invasive Chinook salmon now occur throughout the straits of Chile, and this represents a potential major threat, including impacts from competition, predation and disease introduction. The invasion is expected to expand into other parts of its range (i.e. Argentina). The Chilean salmon aquaculture industry, which is the source of escaped individuals, is expected to expand in the near future. The centre, or the major proportion of its global population is concentrated in the area where this threat is greatest. This threat has been increasing over time, but probably began about 30 years ago. There are no data to quantify population trends at this time; and considering this major threat and the lack of understanding for the likely direct impact, it is listed as Data Deficient. It is highly recommended to conduct studies on population trends as well as the impacts from the invasive salmon. Recommended conservation actions include the continued protection of kelp forests from harvest and to improve management of invasive salmon and prevention of escapes.Fil: Hüne, M.. Universidad Austral de Chile; ChileFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Irigoyen, A.. No especifíca;Fil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Vieira, J.P.. Universidade Federal Do Rio Grande.; Brasi

Champsocephalus esox, Pike Icefish

This demersal species is endemic to the southern Patagonia Sea region where it occurs in kelp forests and fjords. Its physiology restricts it to waters of high oxygen concentration and low temperature, and its survivability is reduced when these conditions fluctuate. Based on survey data and observations of fishers catch, this species has declined by 80% since the 1980s in at least half of its range (the Chilean coast). The status of its population in the other half of its range (Argentina) is poorly understood due to the lack of surveys. Considering the uncertainty regarding its status in the other half of its range, it is conservatively suspected to have declined overall by 30% over the past three generation lengths (12-18 years). Threats include climate change (warming water temperatures), mortality as bycatch in artisanal fisheries and invasive salmon. It is listed as Vulnerable A2bcde. Additional survey work is needed to monitor and understand its population throughout its range. Research is needed on its life history and response to heat shock.Fil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Hüne, M.. Universidad Austral de Chile; ChileFil: Irigoyen, A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Vieira, J.P.. Universidade Federal Do Rio Grande.; Brasi

Harpagifer bispinis

This rocky, intertidal species has a relatively small range, but is common and abundant. There are no known major threats at this time; therefore, it is listed as Least Concern.Fil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Hüne, M.. Universidad Austral de Chile; ChileFil: Irigoyen, A.. No especifíca;Fil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Vieira, J.P.. Universidade Federal Do Rio Grande.; Brasi

Paralichthys isosceles

This demersal species occurs from southern Brazil to Argentina and is taken in multi-species commercial´s fisheries that target demersal fishes through much of its range. It is a relatively minor component of the catch of Paralichthys species as compared to catch of the sympatric P. patagonicus. For purposes of this assessment, half of the global population is considered to occur in Brazil and the other half in Uruguay and Argentina. According to landings and catch per unit effort data, the demersal fish stocks of Brazil are inferred to have declined by at least 30% and possibly to 50%. Due to the lack of specific data for this species, an estimate for population decline is not available or cannot be suspected at this time. According to stock assessment and fisheries data, there is no decline detected in the demersal stock in Argentina and Uruguay and abundance indices show an increase in recent years (since 2014). Fishing effort continues at an unsustainable level in Brazil, the fishery is not well-monitored and conservation measures are insufficient. Conservation measures in Argentina and Uruguay include a total allowable catch limit and regular monitoring of stock status. Based on the potential major threat from overfishing in at least half of its global population, but lack of quantified data, it is listed as Data Deficient with a recommendation to improve fisheries monitoring, including the collection of species-specific data, as" "well as implement conservation measures to reduce effort in Brazilian fisheries.Fil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Vieira, J. P.. Universidade Federal do Rio Grande do Sul; BrasilFil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Irigoyen, A.. No especifíca;Fil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Hüne, M.. Universidad Austral de Chile; Chil

Patagonotothen ramsayi

This species has a relatively small range on the continental shelf and slope of the southern part of the Patagonia Sea where it plays an important ecological role as a prey item for larger marine species. The majority of its global population is concentrated in southern Argentina, including the Malvinas Islands, where the main fishing ground is located. One generation length is estimated as 10 years. It is relatively slow-growing and late to maturity with relatively low fecundity, which may cause it to be susceptible to declines when facing heavy fishing pressure. Previous to 2006, it was mostly discarded as bycatch in large quantities beginning in the 1980s. A large-scale, commercial fishery began in 2007 in the Malvinas area. In areas outside the Malvinas closer to the Argentine mainland, it is taken in fisheries in relatively small amounts. According to stock assessment models based on catch per unit effort data and fishery independent trawl surveys, the estimated biomass for the period of 2005 to 2018 was highest in 2005 and then declined by 79% to a low in 2018. According to the 2019 and 2020 survey results, biomass has continued to decline. Biomass trends prior to 2005 are poorly understood, but based on these data, it is suspected that its population has declined by 40-50% on a global-level over the past one and a half generation lengths, or 15 years. In addition, declines in length at maturity and average length of individuals in the survey catch have also occurred. The cause of decline is poorly understood, but may be attributed in part to fishing activity or a shift in the spatial distribution of its abundance to areas adjacent to the Malvinas. Several fishery management measures are in place, catches have been at a relatively low level and it is not considered overfished. Due to the uncertainty associated with the cause of decline and lack of data prior to 2005, it is not possible to estimate the population trend to cover a three generation length period (either in the past or into the future) at this time. It is listed as Data Deficient with a strong recommendation to conduct studies to improve the understanding of this decline both within the Malvinas area and areas adjacent to it.Fil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Hüne, M.. Universidad Austral de Chile; ChileFil: Irigoyen, A.. No especifíca;Fil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Vieira, J. P.. Universidade Federal Do Rio Grande.; Brasi

Cottoperca trigloides, Frogmouth

This widely distributed, demersal species is associated with rocky bottoms and kelp forests. It is discarded as bycatch in trawl fisheries, but this is not expected to be driving population declines approaching a Near Threatened or threatened level at this time; therefore, it is listed as Least Concern.Fil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Hüne, M.. Universidad Austral de Chile; ChileFil: Irigoyen, A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Vieira, J. P.. Universidade Federal Do Rio Grande.; Brasi

Assessment of total (free and bound) phenolic compounds in spent coffee extracts

Spent coffee is the main byproduct of the brewing process and a potential source of bioactive compounds, mainly phenolic acids easily extracted with water. Free and bound caffeoylquinic (3-CQA, 4-CQA, 5-CQA), dicaffeoylquinic (3,4-diCQA, 3,5-diCQA, 4,5-diCQA), caffeic, ferulic, p-coumaric, sinapic, and 4-hydroxybenzoic acids were measured by HPLC, after the application of three treatments (alkaline, acid, saline) to spent coffee extracts. Around 2-fold higher content of total phenolics has been estimated in comparison to free compounds. Phenolic compounds with one or more caffeic acid molecules were approximately 54% linked to macromolecules such as melanoidins, mainly by noncovalent interactions (up to 81% of bound phenolic compounds). The rest of the quantitated phenolic acids were mainly attached to other structures by covalent bonds (62-97% of total bound compounds). Alkaline hydrolysis and saline treatment were suitable to estimate total bound and ionically bound phenolic acids, respectively, whereas acid hydrolysis is an inadequate method to quantitate coffee phenolic acids

Acanthistius patachonicus, Patagonian Grouper

This rocky reef species has a relatively small range from southern Brazil to central Argentina. It is long- lived and the estimated generation length is 28.5 years. Large commercial fisheries targeted spawning aggregations of this species in the 1980s and 1990s until abundance steeply declined to the point where the market was no longer viable and at least four large areas where spawning aggregations were heavily depleted. Currently, it continues to be targeted by artisanal and industrial fisheries. The implementation of effective fishing area closures, both permanent and seasonal, in the El Rincón area is considered to provide a high level of protection for half of the global population of this species. According to fisher interviews, some level of population decline occurred within the past 40 years, or over a little more than one generation length ago. The lack of fisheries data, including a stock assessment, and the low level of understanding of the status of historical and current spawning aggregations prevents the estimation of percent population decline at this time. A secondary threat may be the reduction of habitat quality due to the invasive alga Undaria pinnatifida on shallow reefs, which has spread through much of its range. It is listed as Data Deficient with a strong recommendation to improve fishery monitoring and to conduct studies on spawning aggregations.Fil: Irigoyen, Alejo Joaquin. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Riestra, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Buratti, C.. Instituto Nacional de Investigaciones y Desarrollo Pesquero; ArgentinaFil: Díaz de Astarloa, Juan Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; ArgentinaFil: Hüne, M.. Universidad Austral de Chile; ChileFil: Landaeta, M.. Universidad de Valparaíso; ChileFil: Vieira, J. P.. Universidade Federal Do Rio Grande.; Brasi