Biology subjects

Pereira, W. A.

Publications and source records attributed to Pereira, W. A..

6 recordsLinked to original sources

bioRxiv2024

Deciphering the Soybean Rust Arsenal: Effectorome Studies and Host-Pathogen Interaction (HPI) network in Phakopsora pachyrhizi and Glycine max Pathosystem

Asian soybean rust (ASR), cause by the fungal pathogen Phakopsora pachyrhizi, stands out as the paramount menace to soybean cultivation, resulting in staggering yield decreases that can surpass 90%. Despite extensive endeavors, the development of cultivars endowed with comprehensive or enduring resistance against the myriad pathotypes remains elusive, thereby underscoring the imperative for pioneering improvement tactics. Fungal effectors, orchestrating the infiltration and colonization of hosts, constitute pivotal determinants in the infection cascade, thus emerging as prime targets for unraveling pathogenicity mechanisms. In this investigation, we endeavored to integrate effectoromics analysis with host-pathogen protein-protein interaction networks (HPPI) to delineate the modus operandi of P. pachyrhizi effectors in subverting plant host immunity. By meticulously delineating the repertoire of predicted effectors and prognosticating protein-protein interactions between effectors and soybean target proteins, we discerned pivotal candidate targets. Notably, a repertoire of 324 host proteins was anticipated to engage in interactions with 21 effectors, predominantly hailing from the Lysophospholipase (LysoPLs) cohort. Particularly conspicuous was the identification of a robust effector candidate (PhapaK8108_7408047) implicated in the targeting of 171 soybean proteins. Its functional involvement in RNA splicing, chromatin organization, histone deacetylation, protein stabilization, and protein folding signifies its pivotal role in the infectious process. Furthermore, our endeavor encompassed the categorization of effectors into carbohydrate-active families, illuminating the prominence of Carbohydrate esterases family 12, primarily catalyzing cellulose and xylan degradation. By amalgamating these multifaceted methodologies, our study provides invaluable insights leading to the formulation of more effective ASR molecular strategies, demonstrating its relevance and innovation in the fields of plant pathology and molecular biology.

genomics↗

bioRxiv2023

Color traits of soybean conventional and transgenic cultivars are affected by glyphosate concentrations using digital imaging

Soybean is the most cultivated oilseed crop in the world, with much of the merit obtained in recent years due to genetic improvement in which greater genetic progress can be obtained by improving physiological characteristics, which result in a greater impact on yield. Color spectra can be good indicators of the physiological quality of plants by quantifying the intensity of colors in the RGB spectra, being a non-destructive method that allows optimizing the collection and the number of data. We aimed to identify differences in spectral reflection between conventional, transgenic RR1 and RR2 soybean cultivars under the effect of glyphosate herbicide. The plants were cultivated in five-liter pots in a greenhouse in a randomized block design, following cultural treatments recommended for the soybean crop. Leaves of plants in vegetative stages V1 or V2 were collected and duly identified to compose a second experiment, being then submitted to incubation in plastic trays in which the treatments were organized in a completely randomized design in a 6x6 factorial scheme, with three replications. Glyphosate herbicide doses (0.0, 0.03%, 0.06%, 0.12% and 0.24% AE/ha) were added to the leaf petiole on a cotton pad in order to maintain constant contact with the respective dose. The trays were kept under ambient conditions for 14 days after incubation under 16h-light and 8h-dark of artificial light. Images were collected with a smartphone camera on the 13th day after leaves collection (DAC) in an appropriate studio to maintain adequate lighting, and on the 14th DAC SPAD index data were collected in three locations on the leaf, avoiding the midrib. The images were cropped and then segmented using manual thresholding in which the average values for the red, green and blue channels were extracted. The Excess Red Index (ExR) was calculated using the red and green channels data. The data obtained were analyzed and the significant effects of the model were analyzed by the Skott-Knott test for the cultivar factor and regression models were adjusted for the dose factor. Spearmans correlation was used to verify the relationship between the studied variables. In view of our results, glyphosate affects the chlorophyll of resistant plants when subjected to continuous exposure and at high doses, leading to senescence and that the red channel information can be used to infer the level of interference in the photosynthetic activity of plants subjected to the herbicide.

plant biology↗

bioRxiv2023

The Cucumber Kinome: genome-wide, identification, characterisation and expression analysis of the Cucumis sativus protein kinases in response to Powdery Mildew, Alternaria Leaf Spot and Root-Knot Nematode

It is widely known that protein kinases (PKs) play a fundamental role in regulating various metabolic processes in plants, from development to response to the environment. However, a detailed characterization of this superfamily is still lacking for several species, such as cucumber (Cucumis sativus), especially regarding their involvement in the response to Powdery Mildew (PM) caused by Podosphaera xanthii. This study aimed to characterize the cucumber PK family, shedding light on its genomic distribution, classification, and expression patterns triggered by P. xanthii. The hidden Markov models (HMMs) analysis uncovered 835 PKs in the cucumber kinome, distributed across its seven chromosomes, and categorized into 20 distinct groups and 123 families, with the RLK group being the most abundant. Evidence of tandem duplication of PK genes was also observed, enriching our understanding of cucumber PKs. To investigate the expression profiles of PK genes in cucumber, we analyzed the transcription levels of all 835 PK genes in RNA-seq data from leaves of resistant and susceptible cultivars of cucumber to P. xanthii, which were artificially inoculated. Depending on the treatment, DEGs ranged from 319 to 1,690, with PK DEGs ranging from 8 to 105. The number of PK DEGs varied between the different contrasts analyzed. Notably, we observed a greater number of PK DEGs in susceptible genotypes when challenged by the pathogen. Our findings indicate the role of specific cucumber PKs in regulating metabolic processes in the context of plant-pathogen interactions and pave the way for further research into the intricate mechanisms underlying cucumber responses to Powdery Mildew. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/532963v3_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@11340b8org.highwire.dtl.DTLVardef@fe1896org.highwire.dtl.DTLVardef@5de8org.highwire.dtl.DTLVardef@1564d0_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

Genome-wide analysis and characterization of theLRR-RLK gene family provides insights intoanthracnose resistance in common bean

Anthracnose, caused by the hemibiotrophic fungus Colletotrichum lindemuthianum, is a damaging disease of common beans that can drastically reduce crop yield. The most effective strategy to manage anthracnose is the use of resistant cultivars. There are many resistance loci that have been identified, mapped and associated with markers in common bean chromosomes. The Leucine-rich repeat kinase receptor protein (LRR-RLK) family is a diverse group of transmembrane receptors, which potentially recognizes pathogen-associated molecular patterns and activates an immune response. In this study, we performed in silico analyses to identify, classify, and characterize common bean LRR-RLKs, also evaluating their expression profile in response to the infection by C. lindemuthianum. By analyzing the entire genome of Phaseolus vulgaris, we could identify and classify 230 LRR-RLKs into 15 different subfamilies. The analyses of gene structures, conserved domains and motifs suggest that LRR-RLKs from the same subfamily are consistent in their exon/intron organization and composition. LRR-RLK genes were found along the 11 chromosomes of the species, including regions of proximity with anthracnose resistance markers. By investigating the duplication events within the LRR-RLK family, we associated the importance of such a family with an expansion resulting from a strong stabilizing selection. Promoter analysis was also performed, highlighting cis elements associated with the plant response to biotic stress. With regard to the expression pattern of LRR-RLKs in response to the infection by C. lindemuthianum, we could point out several differentially expressed genes in this subfamily, which were associated to specific molecular patterns of LRR-RLKs. Our work provides a broad analysis of the LRR-RLK family in P. vulgaris, allowing an in-depth structural and functional characterization of genes and proteins of this family. From specific expression patterns related to anthracnose response, we could infer a direct participation of RLK-LRR genes in the mechanisms of resistance to anthracnose, highlighting important subfamilies for further investigations.

genomics↗

bioRxiv2022

Genome-wide characterization of the common bean kinome: catalog and insights into expression patterns and genetic organization

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

plant biology↗

bioRxiv2020

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs. HighlightThis study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor, providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.

genomics↗