Genetics and Molecular Biology, Bioinformatics, Agricultural and Biological Sciences, Bioenergy
12
Scopus Publications
187
Scholar Citations
6
Scholar h-index
5
Scholar i10-index
Scopus Publications
Influence of biochar on Agave development and on soil characteristics from a brazilian semi-arid region Pedro H. Narciso Ferreira, Nicholas Vinícius Silva, Camila Santos Woloche, Juliet Emília Santos de Sousa, Jean Constantino Gomes da Silva, Gabrielle Henriquetto Cassiano, Victor Henrique Pereira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luís Guilherme Furlan de Abreu Biomass and Bioenergy, 2026
An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems Victor Henrique Pereira, Gabrielle Henriquetto Cassiano, Pedro Henrique Narciso Ferreira, Luís Guilherme Furlan de Abreu, Juliet Emilia Santos de Sousa, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Nicholas Vinícius Silva Microbiology United Kingdom, 2026 The expansion of arid and semi-arid regions, consequent to the intensification of desertification processes attributable to global warming, exerts a deleterious effect on the agricultural production of energy crops, with current estimates indicating that a further 23% of global agricultural areas will suffer from desertification by 2100, precipitating crises in these sectors. Agave species have the capacity to thrive in these marginal environments characterized by aridity and elevated temperatures. These plants can serve as a source of biomass for the production of biofuels, a process that mitigates the environmental impacts of the transport sector while promoting the utilization of drylands, thereby eliminating competition with food crops. Given the paucity of knowledge regarding the soil microbiota and rhizosphere in minimal technological input Agave plantations, the objective of this study was to evaluate the microbiological and chemical soil properties of Agave sisalana and Agave hybrids (H11648 and H400f) farming systems. The analyses, which were carried out using microbial quantification, enzyme stoichiometry and enzymatic vector calculations, demonstrated that the microbiome of these plants is active and well-structured in terms of nutritional acquisition. It was observed that the Agave fields’ microbiome is very similar to that of the native vegetation. This finding suggests that the soil and rhizosphere microbiota are healthy and stable in the Agave fields evaluated, even with the implementation of agronomic exploitation models, as the chemical analysis of the soil reveals that all measured parameters are consistent with those of soils suitable for crop production. These observations persist even in long-established Agave plantations of varying ages that have never received any type of implement or soil correction. Thus, the integration of the chemical and biological data through principal component analysis, redundancy analysis and Permutational Multivariate Analysis of Variance (PERMANOVA) enabled the differentiation of the soil among the three Agave species, which shows the influence of the plant genotype on its microbiota.
Unraveling the mechanisms of ethylene-induced regulation of energy cane shoot and root development Luís Guilherme F. de Abreu, Rodolfo D. Lima Junior, Francisco M. Rivera, Allan Jhonathan R. Ferrari, Nicholas V. Silva, Taícia P. Fill, Eduardo J. Pilau, Mateus B. Fiamenghi, Marcelo F. Carazzolle, Maria Carolina B. Grassi, Gonçalo Amarante G. Pereira, Lucas M. de Carvalho Industrial Crops and Products, 2024
Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple organs of Agave sisalana Lucas M. Carvalho, Nicholas Vinícius Silva, Luís Guilherme F. de Abreu, Marina Püpke Marone, Alexandra Russolo Cardelli, Fabio Trigo Raya, Guido Araújo, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira Frontiers in Chemical Engineering, 2023 Agave plants are well-known for their drought resilience and commercial applications. Among them, Agave sisalana (sisal) is the species most used to produce hard fibers, and it is of great importance for semiarid regions. Agaves also show potential as bioenergy feedstocks, as they can accumulate large amounts of biomass and fermentable sugar. This study aimed to reconstruct the A. sisalana interactome, and identify key genes and modules involved in multiple plant tissues (root, stem, and leaf) through RNA-Seq analysis. We integrated A. sisalana transcriptome sequences and gene expression generated from stem, leaf, and root tissues to build global and conditional co-expression networks across the entire transcriptome. By combining the co-expression network, module classification, and function enrichment tools, we identified 20 functional modules related to at least one A. sisalana tissue, covering functions such as photosynthesis, leaf formation, auxin-activated signaling pathway, floral organ abscission, response to farnesol, brassinosteroid mediated signaling pathway, and light-harvesting. The final interactome of A. sisalana contains 2,582 nodes and 15,083 edges. In the reconstructed interactome, we identified submodules related to plant processes to validate the reconstruction. In addition, we identified 6 hub genes that were searched for in the co-expression modules. The intersection of hub genes identified by both the protein-protein interaction networks (PPI networks) and co-expression analyses using gene significance and module membership revealed six potential candidate genes for key genes. In conclusion, we identified six potential key genes for specific studies in Agave transcriptome atlas studies, biological processes related to plant survival in unfavorable environments and provide strategies for breeding programs.
‘Candidatus Liberibacter asiaticus’ putative effectors: in silico analysis and gene expression in citrus leaves displaying distinct huanglongbing symptoms Laís Moreira Granato, Tiago S. Oliveira, Raquel L. Boscariol-Camargo, Diogo M. Galdeano, Nicholas V. Silva, Heros J. Máximo, Ronaldo J. D. Dalio, Marcos A. Machado Tropical Plant Pathology, 2020 Huanglongbing (HLB) is considered the most devastating bacterial disease in citriculture. It is caused by the phloem-limited α-proteobacterium ‘Candidatus Liberibacter asiaticus’ (CLas). All citrus varieties are susceptible to HLB and many studies have been conducted in an attempt to identify potential targets involved in bacterial virulence and pathogenicity mechanisms. One of the most important virulence factors of bacterial pathogens is the effector molecule that can modify host cell structures, facilitate infection, and/or trigger host defense responses. In this study, 14 CLas candidates for secreted hypothetical proteins were predicted by a bioinformatics pipeline, one of which (NSEC01) was predicted to carry a nuclear localization sequence (NLS). Putative effectors HLBSP04 and HLBSP21 were conserved in all genomes evaluated, whereas HLBSP01, HLBSP19, and HLBSP30 were exclusively found in CLas. Expression analysis of candidate effector genes was performed in citrus leaves exhibiting five distinct HLB symptoms (asymptomatic, blotchy mottle, zinc deficiency, yellowed veins, and vein corky) and used as a guide for the selection of effectors for further functional studies. Genes coding for candidate effectors HLBSP13, HLBSP20, HLBSP28, and NSEC01 had high expression levels in blotchy mottle leaves, suggesting they could be used as marker genes that may facilitate detection of the pathogen in trees with this HLB symptom. As NSEC01 was exclusively found in this work, it was selected for transient expression in Nicotiana benthamiana leaves, but further investigations need to be carried out. Also, other candidate effectors predicted in this work still need to be functionally characterized. This study allowed discussing and proposing hypotheses about CLas classification according to virulence and lifestyle, which can help understand the citrus-CLas interaction.
Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host Carolina Munari Rodrigues, Marco Aurélio Takita, Nicholas Vinicius Silva, Marcelo Ribeiro-Alves, Marcos Antonio Machado BMC Genomics, 2019 BackgroundCitrus are among the most important crops in the world. However, there are many diseases that affect Citrus caused by different pathogens. Citrus also hosts many symbiotic microorganisms in a relationship that may be advantageous for both organisms. The fungi Phyllosticta citricarpa, responsible for citrus black spot, and Phyllosticta capitalensis, an endophytic species, are examples of closely related species with different behavior in citrus. Both species are always biologically associated and are morphologically very similar, and comparing their genomes could help understanding the different lifestyles. In this study, a comparison was carried to identify genetic differences that could help us to understand the biology of P. citricarpa and P. capitalensis.ResultsDrafts genomes were assembled with sizes close to 33 Mb for both fungi, carrying 15,206 and 14,797 coding sequences for P. citricarpa and P. capitalensis, respectively. Even though the functional categories of these coding sequences is similar, enrichment analysis showed that the pathogenic species presents growth and development genes that may be necessary for the pathogenicity of P. citricarpa. On the other hand, family expansion analyses showed the plasticity of the genome of these species. Particular families are expanded in the genome of an ancestor of P. capitalensis and a recent expansion can also be detected among this species. Additionally, evolution could be driven by environmental cues in P. citricarpa.ConclusionsThis work demonstrated genomic differences between P. citricarpa and P. capitalensis. Although the idea that these differences could explain the different lifestyles of these fungi, we were not able to confirm this hypothesis. Genome evolution seems to be of real importance among the Phyllosticta isolates and it is leading to different biological characteristics of these species.
Bioinformatics applied to biotechnology: A review towards bioenergy research L.M. de Carvalho, G. Borelli, A.P. Camargo, M.A. de Assis, S.M.F. de Ferraz, M.B. Fiamenghi, J. José, L.S. Mofatto, S.T. Nagamatsu, G.F. Persinoti, N.V. Silva, A.A. Vasconcelos, G.A.G. Pereira, M.F. Carazzolle Biomass and Bioenergy, 2019
Influence of biochar on Agave development and on soil characteristics from a brazilian semi-arid region PHN Ferreira, NV Silva, CS Woloche, JES de Sousa, JCG da Silva, ... Biomass and Bioenergy 205, 108497 , 2026 2026 Citations: 1
An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems VH Pereira, GH Cassiano, PHN Ferreira, LGF Abreu, JES Souza, ... Access Microbiology, 001065. v2 , 2025 2025
Transcriptomic profiling during the initial hours of axillary bud outgrowth reveals genotype-specific responses in energy cane and sugarcane LGF de Abreu, NV Silva, FM Rivera, AA Vasconcelos, PHN Ferreira, ... Gene Reports 38, 102149 , 2025 2025
Composição e/ou solução bioestimulante, seu uso e método para crescimento de plantas e aumento de biomassa LGF 2. DE ABREU, NV SILVA, FM OLIVEIRA, GH CASSIANO, PK SILVA, ... BR Patent BR1,020,250,023,717 , 2025 2025
Unraveling the mechanisms of ethylene-induced regulation of energy cane shoot and root development LGF de Abreu, RDL Junior, FM Rivera, AJR Ferrari, NV Silva, TP Fill, ... Industrial Crops and Products 222, 119675 , 2024 2024 Citations: 1
Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple organs of Agave sisalana LM Carvalho, NV Silva, LGF de Abreu, MP Marone, AR Cardelli, FT Raya, ... Frontiers in Chemical Engineering 5, 1175235 , 2023 2023 Citations: 4
Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple tissues of Agave sisalana LM de Carvalho, NV Silva, LGF de Abreu, MP Marone, AR Cardelli, ... 2022
Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids K Yanagui, ELO Camargo, LGF de Abreu, ST Nagamatsu, MB Fiamenghi, ... Gene 828, 146476 , 2022 2022 Citations: 7
Desvendando o papel do flavonoide trans-chalcona no crescimento e desenvolvimento de plantas NV Silva Universidade Estadual de Campinas - Unicamp , 2022 2022
Metabolite profiles of energy cane and sugarcane reveal different strategies during the axillary bud outgrowth LGF de Abreu, NV Silva, AJR Ferrari, LM de Carvalho, MB Fiamenghi, ... Plant Physiology and Biochemistry 167, 504-516 , 2021 2021 Citations: 12
Metabolite Profiles of Energy Cane and Sugarcane Reveal Different Strategies During the Axillary Bud Outgrowth A LFd, N Silva, AR Ferrari, C Ld, MF Carazzolle, TP Fill, E Pilau, ... 2020
Influência da suplementação por flavonoide no crescimento de clones comerciais de E. urophylla e E. Urograndis NV Silva, LS Mofatto, MT Rebouças, LM de Carvalho, ST Nagamatsu, ... Influência da suplementação por flavonoide no crescimento de clones … , 2020 2020
Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis , two fungi species that share the same host CM Rodrigues, MA Takita, NV Silva, M Ribeiro-Alves, MA Machado BMC genomics 20 (1), 554 , 2019 2019 Citations: 25
Bioinformatics applied to biotechnology: a review towards bioenergy research MFC L.M. de Carvalho, G. Borelli, A.P. Camargo, M.A. de Assis, S.M.F. de ... Biomass and Bioenergy 123, 195-224 , 2019 2019 Citations: 41
Composições fertilizantes e uso das mesmas NV SILVA, MT REBOUCAS, GAG PEREIRA, J LEPIKSON-NETO, ... BR Patent BR1,020,180,158,325 , 2018 2018
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects DM Magalhães, LLS Scholte, NV Silva, GC Oliveira, C Zipfel, MA Takita, ... BMC genomics 17 (1), 623 , 2016 2016 Citations: 54
Type II Toxin-Antitoxin Distribution and Adaptive Aspects on Xanthomonas Genomes: Focus on Xanthomonas citri PMM Martins, MA Machado, NV Silva, MA Takita, AA De Souza Frontiers in microbiology 7, 652 , 2016 2016 Citations: 32
Número de Fêmeas de Trichospilus diatraeae (Hymenoptera: Eulophidae) para o Controle de Diatraea saccharalis (Lepidoptera: Crambidae) em Cana-de-Açúcar EL VARGAS, FF PEREIRA, VRF CALADO, DF GLAESER, NV SILVA Cadernos de Agroecologia [Volumes 1 (2006) a 12 (2017)] 9 (4) , 2014 2014
Densidade de fêmeas de Trichospilus diatraeae (Hymenoptera: Eulophidae) por pupa de Diatraea saccharalis (Lepidoptera: Crambidae) EL Vargas, FF Pereira, VRF Calado, DF Glaeser, BAC Rodrigues, ... Sitientibus série Ciências Biológicas 13 , 2013 2013 Citations: 6
MOST CITED SCHOLAR PUBLICATIONS
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects DM Magalhães, LLS Scholte, NV Silva, GC Oliveira, C Zipfel, MA Takita, ... BMC genomics 17 (1), 623 , 2016 2016 Citations: 54
Bioinformatics applied to biotechnology: a review towards bioenergy research MFC L.M. de Carvalho, G. Borelli, A.P. Camargo, M.A. de Assis, S.M.F. de ... Biomass and Bioenergy 123, 195-224 , 2019 2019 Citations: 41
Type II Toxin-Antitoxin Distribution and Adaptive Aspects on Xanthomonas Genomes: Focus on Xanthomonas citri PMM Martins, MA Machado, NV Silva, MA Takita, AA De Souza Frontiers in microbiology 7, 652 , 2016 2016 Citations: 32
Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis , two fungi species that share the same host CM Rodrigues, MA Takita, NV Silva, M Ribeiro-Alves, MA Machado BMC genomics 20 (1), 554 , 2019 2019 Citations: 25
Metabolite profiles of energy cane and sugarcane reveal different strategies during the axillary bud outgrowth LGF de Abreu, NV Silva, AJR Ferrari, LM de Carvalho, MB Fiamenghi, ... Plant Physiology and Biochemistry 167, 504-516 , 2021 2021 Citations: 12
Internode elongation in energy cane shows remarkable clues on lignocellulosic biomass biosynthesis in Saccharum hybrids K Yanagui, ELO Camargo, LGF de Abreu, ST Nagamatsu, MB Fiamenghi, ... Gene 828, 146476 , 2022 2022 Citations: 7
Densidade de fêmeas de Trichospilus diatraeae (Hymenoptera: Eulophidae) por pupa de Diatraea saccharalis (Lepidoptera: Crambidae) EL Vargas, FF Pereira, VRF Calado, DF Glaeser, BAC Rodrigues, ... Sitientibus série Ciências Biológicas 13 , 2013 2013 Citations: 6
Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple organs of Agave sisalana LM Carvalho, NV Silva, LGF de Abreu, MP Marone, AR Cardelli, FT Raya, ... Frontiers in Chemical Engineering 5, 1175235 , 2023 2023 Citations: 4
Influence of biochar on Agave development and on soil characteristics from a brazilian semi-arid region PHN Ferreira, NV Silva, CS Woloche, JES de Sousa, JCG da Silva, ... Biomass and Bioenergy 205, 108497 , 2026 2026 Citations: 1
Unraveling the mechanisms of ethylene-induced regulation of energy cane shoot and root development LGF de Abreu, RDL Junior, FM Rivera, AJR Ferrari, NV Silva, TP Fill, ... Industrial Crops and Products 222, 119675 , 2024 2024 Citations: 1
An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems VH Pereira, GH Cassiano, PHN Ferreira, LGF Abreu, JES Souza, ... Access Microbiology, 001065. v2 , 2025 2025
Transcriptomic profiling during the initial hours of axillary bud outgrowth reveals genotype-specific responses in energy cane and sugarcane LGF de Abreu, NV Silva, FM Rivera, AA Vasconcelos, PHN Ferreira, ... Gene Reports 38, 102149 , 2025 2025
Composição e/ou solução bioestimulante, seu uso e método para crescimento de plantas e aumento de biomassa LGF 2. DE ABREU, NV SILVA, FM OLIVEIRA, GH CASSIANO, PK SILVA, ... BR Patent BR1,020,250,023,717 , 2025 2025
Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple tissues of Agave sisalana LM de Carvalho, NV Silva, LGF de Abreu, MP Marone, AR Cardelli, ... 2022
Desvendando o papel do flavonoide trans-chalcona no crescimento e desenvolvimento de plantas NV Silva Universidade Estadual de Campinas - Unicamp , 2022 2022
Metabolite Profiles of Energy Cane and Sugarcane Reveal Different Strategies During the Axillary Bud Outgrowth A LFd, N Silva, AR Ferrari, C Ld, MF Carazzolle, TP Fill, E Pilau, ... 2020
Influência da suplementação por flavonoide no crescimento de clones comerciais de E. urophylla e E. Urograndis NV Silva, LS Mofatto, MT Rebouças, LM de Carvalho, ST Nagamatsu, ... Influência da suplementação por flavonoide no crescimento de clones … , 2020 2020
Composições fertilizantes e uso das mesmas NV SILVA, MT REBOUCAS, GAG PEREIRA, J LEPIKSON-NETO, ... BR Patent BR1,020,180,158,325 , 2018 2018
Número de Fêmeas de Trichospilus diatraeae (Hymenoptera: Eulophidae) para o Controle de Diatraea saccharalis (Lepidoptera: Crambidae) em Cana-de-Açúcar EL VARGAS, FF PEREIRA, VRF CALADO, DF GLAESER, NV SILVA Cadernos de Agroecologia [Volumes 1 (2006) a 12 (2017)] 9 (4) , 2014 2014
