Genomics Lab

Chromosome-level comparative genomics and host-specific fungal transcriptomics uncover adaptive virulence strategies in the sugarcane smut pathogen

Wed, 05 Nov 2025 00:00:00 +0000

Transcriptional responses of sugarcane varieties to Pratylenchus zeae infection

Wed, 03 Sep 2025 00:00:00 +0000

New preprint from our group now available on bioRxiv! Check out the abstract in this post.

Our group has just published a preprint on August 30th presenting novel results on the transcriptional responses of two sugarcane varieties to infection by the nematode Pratylenchus zeae. The work is now available on bioRxiv!

Abstract:

The root-lesion nematode Pratylenchus zeae ranks among the most pervasive soilborne threats to global sugarcane (Saccharum spp.) production, however, the molecular basis of host resistance to this pathogen remains largely unexplored. Using comparative transcriptomics 15 days after inoculation, we profiled root response patterns of a resistant cultivar (RB966982) and a susceptible cultivar (CTC9001). Differential gene expression analysis identified 3,385 DEGs (1,426 up, 1,959 down) in the susceptible CTC9001 and 8,689 DEGs (5,334 up, 3,355 down) in the resistant RB966982 when comparing control and inoculated plants, revealing distinct genotype-specific defense strategies. The resistant genotype mounted a coordinated, multilayered defense marked by dramatic transcriptional reprogramming, including intensified glycolysis and fatty-acid biosynthesis, elevated oxidoreductase/ROS activity, and concurrent activation of jasmonic and salicylic acid associated pathways, with strong induction of multiple PR1 homologs. RB966982 also showed pre-primed and inducible resistance gene analogs and targeted cell-wall reinforcement through xyloglucan fucosylation. By contrast, CTC9001 displayed a delayed or attenuated response characterized by cell-proliferation signatures and broad activation of callose-related defenses (1,3-β-D-glucan synthesis) that appear insufficient to limit nematode progression. GO enrichment analysis revealed that the resistant response was dominated by biological processes linked to carbohydrate and lipid metabolism, oxidoreductase activity, hormone signaling, and cell-wall organization, while the susceptible response was enriched in stress-related pathways lacking coordinated metabolic and structural reinforcement. Collectively, these findings indicate that durable resistance to P. zeae is unlikely to arise from a single mechanism, effective protection will require stacking complementary defense layers, including early metabolic reprogramming, robust hormone-mediated signaling, and reinforced cell-wall barriers. The candidate RGAs, PR1 homologs, and cell-wall remodeling enzymes identified here, together with the GO-enriched pathways, provide concrete targets for marker-assisted breeding and gene editing strategies aimed at developing sugarcane cultivars with durable nematode resistance.

Multilayered Defense Responses in Sugarcane Against Pratylenchus zeae Revealed by Comparative Transcriptomics

Sat, 30 Aug 2025 00:00:00 +0000

Integrative Multi-Omics Analysis Reveals Stress-Specific Molecular Architectures in Soybean under Drought and Rust Infection

Tue, 08 Jul 2025 00:00:00 +0000

Updated chromosome-level genome assembly of Sporisorium scitamineum with improved accuracy and completeness

Tue, 27 May 2025 00:00:00 +0000

Transcriptome Profiling of Resistance Genes Analogs in Soybean’s Cross-Tolerance to Water Limitation and Rust Stress

Fri, 23 May 2025 00:00:00 +0000

Exploring Potential Surrogate Systems for Studying the Early Steps of the Sporisorium scitamineum Pathogenesis

Sat, 01 Jun 2024 00:00:00 +0000

First investigation into the genetic control of meiosis in sugarcane

Sat, 01 Jun 2024 00:00:00 +0000

CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane

Mon, 08 Jan 2024 00:00:00 +0000

Water Limitation Causes Early-Stage Metabolic Perturbation in the Interaction of Soybean and the Causal Agent of Asian Soybean Rust

Mon, 01 Jan 2024 00:00:00 +0000

Transmission of Xanthomonas albilineans by the spittlebug, Mahanarva fimbriolata (Hemiptera: Cercopidae), in Brazil: first report of an insect vector for the causal agent of sugarcane leaf scald

Wed, 01 Nov 2023 00:00:00 +0000

Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease

Sun, 01 Jan 2023 00:00:00 +0000

Contact

Mon, 24 Oct 2022 00:00:00 +0000

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Mon, 24 Oct 2022 00:00:00 +0000

A Bacterial Type Three Secretion-Based Delivery System for Functional Characterization of Sporisorium scitamineum Plant Immune Suppressing Effector Proteins

Fri, 01 Jul 2022 00:00:00 +0000

A genome sequence resource for the genus Passiflora , the genome of the wild diploid species Passiflora organensis

Mon, 01 Nov 2021 00:00:00 +0000

Arabidopsis-Based Dual-Layered Biological Network Analysis Elucidates Fully Modulated Pathways Related to Sugarcane Resistance on Biotrophic Pathogen Infection

Thu, 19 Aug 2021 00:00:00 +0000

Complete Chromosome-Scale Genome Sequence Resource for Sporisorium panici-leucophaei , the Causal Agent of Sourgrass Smut Disease

Thu, 01 Apr 2021 00:00:00 +0000

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

Thu, 11 Mar 2021 00:00:00 +0000

Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors

Fri, 04 Dec 2020 00:00:00 +0000

Differential responses of genes and enzymes associated with ROS protective responses in the sugarcane smut fungus

Tue, 01 Dec 2020 00:00:00 +0000

Multiple resistance of Plasmopara viticola to QoI and CAA fungicides in Brazil

Tue, 01 Dec 2020 00:00:00 +0000

Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility

Wed, 01 Jul 2020 00:00:00 +0000

Characterization of genes responsive to osmotic and oxidative stresses of the sugarcane bacterial pathogen Leifsonia xyli subsp. xyli

Sun, 01 Mar 2020 00:00:00 +0000

Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum

Sun, 01 Dec 2019 00:00:00 +0000

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

Sun, 01 Dec 2019 00:00:00 +0000

Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen

Thu, 20 Jun 2019 00:00:00 +0000

Assessing early resistance responses of sugarcane to Xanthomonas albilineans

Tue, 01 Jan 2019 00:00:00 +0000

Proteome characterization of the cell wall, apoplast and extracellular space of sugarcane infected with Sporisorium scitamineum, the causal agent of smut disease

Tue, 01 Jan 2019 00:00:00 +0000

Novel Insights Into the Early Stages of Ratoon Stunting Disease of Sugarcane Inferred from Transcript and Protein Analysis

Sat, 01 Dec 2018 00:00:00 +0000

Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations

Thu, 14 Jun 2018 00:00:00 +0000

Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization

Fri, 06 Apr 2018 00:00:00 +0000

Progress in understanding fungal diseases affecting sugarcane: smut

Mon, 05 Mar 2018 00:00:00 +0000

Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission

Wed, 31 May 2017 00:00:00 +0000

Functional analysis of oxidative burst in sugarcane smut-resistant and -susceptible genotypes

Sat, 01 Apr 2017 00:00:00 +0000

Genome-wide characterization of alternative splicing patterns in sugarcane modulated during infection with smut pathogen, Sporisorium scitamineum

Sun, 01 Jan 2017 00:00:00 +0000

Molecular variability and genetic relationship among Brazilian strains of the sugarcane smut fungus

Thu, 01 Dec 2016 00:00:00 +0000

Sporisorium scitamineum colonisation of sugarcane genotypes susceptible and resistant to smut revealed by GFP

Tue, 01 Nov 2016 00:00:00 +0000

RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease

Thu, 01 Sep 2016 00:00:00 +0000

Sugarcane smut: shedding light on the development of the whip-shaped sorus

Sat, 27 Aug 2016 00:00:00 +0000

Development of a qPCR for Leifsonia xyli subsp. xyli and quantification of the effects of heat treatment of sugarcane cuttings on Lxx

Mon, 01 Feb 2016 00:00:00 +0000

A stable Leifsonia xyli subsp. xyli GFP tagged strain reveals a new colonization niche in sugarcane tissues

Fri, 01 Jan 2016 00:00:00 +0000

Analysis of plant gene expression during passion fruit Xanthomonas axonopodis interaction implicates lipoxygenase 2 in host defence

Wed, 01 Jul 2015 00:00:00 +0000

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

Fri, 12 Jun 2015 00:00:00 +0000

Mon, 01 Jan 0001 00:00:00 +0000