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Chloroplast metabolism is very sensitive to environmental fluctuations and is intimately related to plant leaf development. Characterization of the chloroplast proteome dynamics can contribute to a better understanding on plant adaptation to different climate scenarios and leaf development processes. Herein, we carried out a discovery-driven analysis of the Eucalyptus grandis chloroplast proteome during leaf maturation and throughout different seasons of the year. The chloroplast proteome from young leaves differed the most from all assessed samples. Most upregulated proteins identified in mature and young leaves were those related to catabolic-redox signaling and biogenesis processes, respectively. Seasonal dynamics revealed unique proteome features in the fall and spring periods. The most abundant chloroplast protein in humid (wet) seasons (spring and summer) was a small subunit of RuBisCO, while in the dry periods (fall and winter) the proteins that showed the most pronounced accumulation were associated with photo-oxidative damage, Calvin cycle, shikimate pathway, and detoxification. Our investigation of the chloroplast proteome dynamics during leaf development revealed significant alterations in relation to the maturation event. Our findings also suggest that transition seasons induced the most pronounced chloroplast proteome changes over the year. This study contributes to a more comprehensive understanding on the subcellular mechanisms that lead to plant leaf adaptation and ultimately gives more insights into Eucalyptus grandis phenology.

Polyploidy is an event that culminates with the condition of having two or more pairs of homologous chromosomes. Here we used proteomics to unveil the differential gene expression in Eucalyptus urophylla x Eucalyptus grandis polyploids, and its isogenic diploid, when plants were challenged against high temperature and elevated CO2 concentration. Growth under high temperature induced an increase in the leaf area, a phenotypic pattern further increased when plants were cultivated in both high temperature and elevated CO2, but inversely for stem branching. Global proteome analysis indicated the absence of a clear pattern of proteome similarities between genotypes, suggesting a unique differential genome regulation would only occur upon environmental stimulus. We concluded that the polyploidy effects in Eucalyptus genotypes are mostly revealed when influenced by environment, that the proteome responses are genotype dependent and that the changes in the gene expression are more pronounced when plants are cultivated in high temperature. RESUMO: Poliploidia é um evento que culmina na condição de ter dois ou mais pares de cromossomos homólogos. Aqui, usamos a proteômica para revelar a expressão gênica diferencial em poliploides de Eucalyptus urophylla x Eucalyptus grandis e seu diploide isogênico, quando as plantas foram desafiadas contra altas temperaturas e concentrações elevadas de CO2. O crescimento sob altas temperaturas induziu um aumento na área foliar, um padrão fenotípico ainda mais acentuado quando as plantas foram cultivadas tanto em altas temperaturas quanto em CO2 elevado, mas inversamente para a ramificação do caule. A análise global do proteoma indicou a ausência de um padrão claro de semelhanças no proteoma entre genótipos, sugerindo que uma regulação gênica diferencial única ocorreria apenas sob estímulo ambiental. Concluímos que os efeitos da poliploidia em genótipos de Eucalyptus são mais revelados quando influenciados pelo ambiente, que as respostas proteômicas são dependentes do genótipo e que as mudanças na expressão gênica são mais pronunciadas quando as plantas são cultivadas em altas temperaturas.

MAC and JP are grateful for award of a Ramón y Cajal (RYC2017-23706) and Juan de la Cierva Incorporación (IJC-2019-040330- I) contracts, respectively, by the Spanish Ministry of Science, Innovation and Universities.

Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.

As one of the world’s top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica ( CSA ) remain unclear. We newly generated 94 Camellia sinensis ( C . sinensis ) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94  C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.

Key message Minor effect on the chloroplast antioxidant proteins was detected in Eucalyptus urophylla cultivated in high-CO 2 atmosphere. Global climate change can significantly alter plant cell metabolism. A higher atmospheric CO 2 scenario may be beneficial for C3 plants through the stimulation of photosynthesis. This predicted increase in the rate of carbon assimilation may also increase the expression of enzymes involved in the antioxidant cellular defense. Here, we studied the responses of the chloroplastic antioxidant system of Eucalyptus urophylla plants cultivated in a high-CO 2 condition. Plants exposed to a high concentration (980 ppm) of CO 2 showed an increase in the H 2 O 2 concentration and MDA content in relation to those cultivated at 410 and 680 ppm. With the discovery proteomics approach used herein, we identified 19 chloroplastic antioxidant proteoforms and pinpointed differentially regulated isoforms of an ascorbate peroxidase and a superoxidase dismutase upon cultivation in a high-CO 2 atmosphere. Our data indicate that the CO 2 stimulus induces only minor changes in the antioxidant metabolism of E. urophylla chloroplasts.

Among the Ctenocephalides felis felis -borne pathogens, Bartonella henselae , the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae -infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae . In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels.

Our previous studies have shown that ‘Palmer’ mangoes immersed in solutions containing 2.5% sorbitol and stored under a controlled atmosphere (CA) at 8 °C for 30 days had fewer symptoms of a chilling injury. However, there is no information regarding the effectiveness of sorbitol treatment in other atmospheres and/or in combination with lower temperatures. Thus, the objective of this study was to assess the impact of dipping ‘Palmer’ mangoes in 0.1% and 2.5% (w/v) sorbitol solutions and storing the fruit under a CA without atmosphere modification (21 kPa O2 + 0.03 kPa CO2) at 8 °C/95% relative humidity (RH) or with 5 kPa O2 + 5 kPa CO2 at 4 °C/95% RH for 28 days. The fruits were evaluated periodically for chilling injuries, quality, and oxidative metabolism. A chilling injury (CI) was correlated with increased fresh weight loss (FWL) and changes in the color of the epicarp (Lpeel, h°peel, and Cpeel) and mesocarp (L*pulp). Lipid peroxidation (LPpulp and LPpeel) and the hydrogen peroxide content (H2O2peel and H2O2pulp) were associated with the development of a CI, particularly after being transferred to ambient. The treatment with 2.5% sorbitol was more effective in minimizing the chilling injury symptoms and did not compromise the fruit quality, especially when it was stored at 4 °C in association with a CA containing 5 kPa O2 + 5 kPa CO2. This treatment reduced lipid peroxidation and increased the activities of the superoxide dismutase (SOD) and ascorbate peroxidase (APX) enzymes in the epicarp and mesocarp, providing greater cold tolerance. The use of 2.5% sorbitol has been identified as the most efficacious approach for mitigating the adverse impacts of chilling injuries, preserving the fruit quality, and enhancing oxidative metabolism, even at lower temperatures. Thus, this treatment represents a viable alternative for managing chilling injuries in mangoes.

Horsetail (Equisetum hyemale) is a widespread vascular plant species, whose reproduction is mainly dependent on the growth and development of the rhizomes. Due to its key evolutionary position, the identification of factors that could be involved in the existence of the rhizomatous trait may contribute to a better understanding of the role of this underground organ for the successful propagation of this and other plant species. In the present work, we characterized the proteome of E. hyemale rhizomes using a GeLC-MS spectral-counting proteomics strategy. A total of 1,911 and 1,860 non-redundant proteins were identified in the rhizomes apical tip and elongation zone, respectively. Rhizome-characteristic proteins were determined by comparisons of the developing rhizome tissues to developing roots. A total of 87 proteins were found to be up-regulated in both horsetail rhizome tissues in relation to developing roots. Hierarchical clustering indicated a vast dynamic range in the regulation of the 87 characteristic proteins and revealed, based on the regulation profile, the existence of nine major protein groups. Gene ontology analyses suggested an over-representation of the terms involved in macromolecular and protein biosynthetic processes, gene expression, and nucleotide and protein binding functions. Spatial difference analysis between the rhizome apical tip and the elongation zone revealed that only eight proteins were up-regulated in the apical tip including RNA-binding proteins and an acyl carrier protein, as well as a KH domain protein and a T-complex subunit; while only seven proteins were up-regulated in the elongation zone including phosphomannomutase, galactomannan galactosyltransferase, endoglucanase 10 and 25, and mannose-1-phosphate guanyltransferase subunits alpha and beta. This is the first large-scale characterization of the proteome of a plant rhizome. Implications of the findings were discussed in relation to other underground organs and related species.

Polyploidy is an event that culminates with the condition of having two or more pairs of homologous chromosomes. Here we used proteomics to unveil the differential gene expression in Eucalyptus urophylla x Eucalyptus grandis polyploids, and its isogenic diploid, when plants were challenged against high temperature and elevated C[O.sub.2] concentration. Growth under high temperature induced an increase in the leaf area, a phenotypic pattern further increased when plants were cultivated in both high temperature and elevated C[O.sub.2], but inversely for stem branching. Global proteome analysis indicated the absence of a clear pattern of proteome similarities between genotypes, suggesting a unique differential genome regulation would only occur upon environmental stimulus. We concluded that the polyploidy effects in Eucalyptus genotypes are mostly revealed when influenced by environment, that the proteome responses are genotype dependent and that the changes in the gene expression are more pronounced when plants are cultivated in high temperature. Key words: climate change, genome duplication, genotype-phenotype relationship, plant-environment interaction. Poliploidia é um evento que culmina na condição de ter dois ou mais pares de cromossomos homólogos. Aqui, usamos a proteômica para revelar a expressão gênica diferencial em poliploides de Eucalyptus urophylla x Eucalyptus grandis e seu diploide isogênico, quando as plantas foram desafiadas contra altas temperaturas e concentrações elevadas de C[O.sub.2]. O crescimento sob altas temperaturas induziu um aumento na área foliar, um padrão fenotípico ainda mais acentuado quando as plantas foram cultivadas tanto em altas temperaturas quanto em C[O.sub.2] elevado, mas inversamente para a ramificação do caule. A análise global do proteoma indicou a ausência de um padrão claro de semelhanças no proteoma entre genótipos, sugerindo que uma regulação gênica diferencial única ocorreria apenas sob estímulo ambiental. Concluímos que os efeitos da poliploidia em genótipos de Eucalyptus são mais revelados quando influenciados pelo ambiente, que as respostas proteômicas são dependentes do genótipo e que as mudanças na expressão gênica são mais pronunciadas quando as plantas são cultivadas em altas temperaturas. Palavras-chave: mudança climática, duplicação do genoma, relação genótipo-fenótipo, interação planta-ambiente.