Anete Pereira de Souza

Multi-omics integration reveals candidate genes and molecular mechanisms associated with resistance to sugarcane smut

The paper integrates association mapping and transcriptomics to identify candidate genes and molecular mechanisms associated with sugarcane resistance to smut.

Assessing the Role of Marker Density and Minor Allele Frequency on Machine Learning Driven Genomic Selection Accuracy in Grapevine

This study evaluates how marker density and minor allele frequency affect genomic selection accuracy in grapevine using machine learning models and conventional methods.

Genome-wide association study in a diverse grapevine collection provides insights into the genetic basis of berry size and cluster architecture traits

This study performs a GWAS on a diverse grapevine collection to identify genetic determinants of berry size and cluster architecture traits, finding significant SNPs and candidate genes.

Multiple mating predicts queen reproductive output in the polygynous Neotropical trap-jaw ant, Odontomachus chelifer (Formicidae: Ponerinae)

This study investigates factors affecting queen reproductive output in O. chelifer ants, finding that multiple mating positively correlates with reproductive success.

Multiomic insights into sucrose accumulation in sugarcane

This study uses multiomic approaches to identify genetic variants and genes associated with sucrose accumulation in sugarcane, providing insights for breeding and biotechnology.

Sugarcane yellow leaf virus impairs the transcriptomic defense responses of sugarcane to its new aphid vector Melanaphis sorghi

This study investigates how Sugarcane yellow leaf virus (SCYLV) affects sugarcane's transcriptomic defense responses to its aphid vector Melanaphis sorghi, identifying key gene pathways and regulatory hubs.

Genetic response to light and carbon source variations in Trichoderma harzianum: The key regulatory roles of env1, cre1, and blr2

This study investigates how light and carbon sources affect gene expression in Trichoderma harzianum, identifying env1, cre1, and blr2 as key regulators of metabolic adaptation.

Identifying Candidate Genes for Sugar Accumulation in Sugarcane Cultivars: From a Syntenic Genomic Region to a Gene Coexpression Network

The paper identifies three candidate genes for sugar accumulation in sugarcane using synteny analysis, BAC library screening, RNA-seq, and coexpression network analysis.

Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits in Urochloa ruziziensis

This study uses genome-wide family prediction to identify markers associated with agronomic traits in Urochloa ruziziensis and links them to molecular mechanisms.

Targeting lignocellulolytic gene clusters in novel Trichoderma atroviride and Trichoderma harzianum strains through Bac-guided analysis

The paper identifies novel lignocellulolytic gene clusters in Trichoderma species by analyzing genomic regions enriched in degradative enzymes using BAC methodology and RNA-seq data.

Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis

This paper develops the highest-density linkage map for hexaploid Urochloa humidicola, revealing genetic organization, apomixis, and polyploid origins using SNP markers.

Uncovering the molecular signatures of russet skin formation in Niagara grapevine (Vitis vinifera x Vitis labrusca)

The paper identifies molecular signatures associated with russet skin formation in Niagara grapevine by analyzing transcriptomic and histological differences between somatic variants.

Whole-Genome Sequencing and Comparative Genomic Analysis of Potential Biotechnological Strains of Trichoderma harzianum, Trichoderma atroviride, and Trichoderma reesei

The paper performs whole-genome sequencing and comparative genomic analysis of Trichoderma strains to assess genetic diversity and identify structural variants.

Genetic diversity, population structure and parentage analysis of Brazilian grapevine hybrids after half a century of genetic breeding

The paper analyzes genetic diversity and parentage of Brazilian grapevine hybrids to assess genetic erosion and guide breeding programs.

Genome-wide association reveals novel insights into the molecular mechanisms regulating stem volume in Pinus taeda

The paper identifies SNPs and genes associated with stem volume in loblolly pine using GWAS and machine learning, revealing regulatory mechanisms and candidate genes for growth traits.

A divide-and-conquer approach for genomic prediction in rubber tree using machine learning

This paper develops a machine learning approach for predicting rubber tree stem circumference using molecular markers, achieving higher accuracy than traditional models in a single-environment scenario.

A joint learning approach for genomic prediction in polyploid grasses

This paper develops a joint learning approach to improve genomic prediction in polyploid grasses, achieving over 50% accuracy improvements over traditional methods.

Network Analysis Reveals Different Cellulose Degradation Strategies across Trichoderma harzianum Strains Associated with XYR1 and CRE1

The paper compares cellulose degradation strategies in two Trichoderma harzianum strains using network analysis, revealing strain-specific regulatory differences involving XYR1 and CRE1.

Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

This study assesses genome-wide diversity in traditional Brazilian manioc varieties, identifying selective signatures and high neutral genetic diversity across biomes.

Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane

The paper identifies differentially expressed genes related to sucrose metabolism and cell wall biosynthesis in sugarcane apical culms across developmental stages and genotypes.

Genomic prediction with allele dosage information in highly polyploid species

This study improves genomic selection in highly polyploid species by incorporating allele dosage and dominance effects, showing significant gains in predictive ability in certain conditions.

A deeper cascade of mechanisms involved in cold resistance in Hevea brasiliensis

The paper identifies gene expression patterns and regulatory mechanisms in cold-resistant rubber tree clones using RNA-seq and gene coexpression network analysis.

Unravelling complex molecular mechanisms in pine with genome-wide association analysis and gene co-expression networks

The paper was withdrawn due to changes in phenotypic focus, and no findings are presented.

An Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses

This paper introduces an automated SNP-based method to identify contaminants in polyploid plant progenies using PCA, Mendelian segregation analysis, and clustering, validated on simulated and real data.

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

This study profiles the kinomes of sugarcane and sorghum, identifying PKs and their evolutionary relationships, and provides expression patterns and coexpression networks.

The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation

This study identifies synergistic gene and protein interactions in Trichoderma harzianum for cellulose degradation using transcriptomic and proteomic analyses.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance

The paper uses machine learning to identify genomic regions associated with sugarcane brown rust resistance by analyzing SNP data from full-sib progeny.

Geographical and environmental contributions to genomic divergence in mangrove forests

This study examines how geographical and environmental factors influence genetic variation in two mangrove species along the South American coast, revealing distinct patterns of gene flow and isolation-by-environment.

Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)

The paper identifies CAZymes, transcription factors, and transporters in Trichoderma harzianum IOC3844 involved in cellulose degradation using genomic, transcriptomic, and exoproteomic data.

Genetic structure and molecular diversity of Brazilian grapevine germplasm: management and use in breeding programs

This study characterizes the genetic diversity of 410 Brazilian grapevine accessions using microsatellite markers, identifies a core collection, and highlights applications for breeding programs.