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Gouthaman Puthan Purayil, PhD

Research Associate & Bioinformatician

Specializing in comparative genomics, transcriptomics, genome assembly, and plant–microbe interactions. Resolving chromosome-level reference assemblies and genomic mechanisms regulating crop resilience and host-pathogen dynamics.

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5 H-index
139 Citations
9 Publications
Genomic Circular Plot (Circos Mock)
Methodology & Scope

Interdisciplinary Research Focus

Bridging computational workflows with molecular validations to untangle plant, bacterial, and fungal interactions.

Comparative Genomics & Pipelines

High-throughput sequence assembly and transcriptome modeling.

Designing scalable Nextflow and Linux CLI workflows to parse complex eukaryotic and prokaryotic genomes. Resolving chromosome-scale plant and fungal pathogen genomes using long-reads (ONT, PacBio) combined with physical mapping (Hi-C, Omni-C) and transcriptome profiling.

  • Transcriptomics: RNA-Seq analysis, differential gene expression (DESeq2, edgeR), and network clustering.
  • Genome Assembly: Chromosome-scale assembly, scaffolding, repeat masking, structural annotation (MAKER, BRAKER).
Python R Nextflow Docker DESeq2 Hi-C Scaffolding STAR Orthofinder
pipeline_status.log ● active
crowmane@uaeu:~$ nflow run genomic-assembly --reads fastq/
Launching Nextflow pipeline v2.4.0...
[1/4] Running Quality Assessment: FastQC/MultiQC... Done.
[2/4] Scaffolding with Omni-C physical contact map... Done.
[3/4] Running Ab-initio Gene Prediction (BRAKER3)...
- Processing protein hints against plants database...
- Predicted genes count: 18,349
[4/4] Generating Annotation report (InterProScan)...

Molecular Validation & Bioassays

Validating in-silico profiles in vivo with bench assays.

Coupling genomic studies with functional experiments. Assessing rhizosphere-competent actinobacteria consortiums under salinity and heavy-metal stress conditions in crops like date palm, tomato, and corn.

  • Assays: RT-qPCR validation, cloning, plant tissue culture, biocontrol screening.
  • Microbiology: Cultivation, identification, and physiological testing of plant growth-promoting actinobacteria.
RT-qPCR ONT MinION DNBSEQ Tissue Culture Microscopy Western Blot
Differential Expression Heatmap (RNA-Seq) Gene Expression Profile
Hover over cells to view transcript fold change log2(FC)
Research Output

Selected Publications & Projects

A collection of research projects and peer-reviewed articles focusing on genomic analysis, pathogen defense, and biological control.

Q1 Publication Journal of Experimental Botany (2026)

Time-resolved transcriptome analysis reveals molecular signatures of Fusarium proliferatum DSM106835-induced sudden decline syndrome in date palm (Phoenix dactylifera L.)

Investigated spatial and temporal transcriptomic responses of date palm to Fusarium proliferatum, discovering host defense genes and key pathogen virulence profiles.

Transcriptomics RNA-Seq Fungi IF: 6.5
View DOI
Correction Frontiers in Plant Science (2026)

Correction: The 1-aminocyclopropane-1-carboxylic acid deaminase-producing Streptomyces violaceoruber UAE1 can provide protection from sudden decline syndrome on date palm

Formal correction update addressing taxonomic designation of the biocontrol strain Streptomyces to S. tendae UAE1 and refining molecular ACCD activity references.

Correction Taxonomy Biocontrol Streptomyces
View DOI
Q1 Publication BMC Plant Biology (2025)

Rhizosphere-competent actinobacterial consortium alleviates salinity stress in tomato through plant growth-promoting traits and ACC deaminase activity

Demonstrated that inoculation with a tailored rhizosphere actinobacterial consortium mitigates high salinity stress in Solanum lycopersicum, improving physiology and stress-gene expression.

Salinity Stress Tomato Actinobacteria IF: 5.6
View DOI
Q1 Publication Biology and Fertility of Soils (2025)

Rhizosphere-competent actinobacteria with ACC deaminase activity mitigate heavy metal stress in corn (Zea mays)

Explored how ACC deaminase-producing rhizosphere-competent actinobacteria alleviate lead and heavy metal toxicity in corn, improving overall agronomic indices.

Heavy Metals Corn ACC Deaminase IF: 6.6
View DOI
Postdoc Project UAEU-KCGEB Funded (2025)

Functional genomics of stress resilience in UAE crops

Mapping plant-microbe signaling during abiotic stresses (drought, salinity) using multi-omics tools to formulate microbial inoculants tailored for arid environments.

Postdoc Multi-omics Crop resilience
Project Plan
Q1 Publication Scientific Data (2024)

A high-quality genome assembly and annotation of Thielaviopsis punctulata DSM102798

Generated a chromosome-scale reference assembly of the date palm pathogen Thielaviopsis punctulata using Hi-C scaffolding, yielding the foundation for black scorch disease GWAS.

Genomics Hi-C Assembly IF: 7.2
View DOI
Q1 Publication Scientific Data (2023)

Fully resolved assembly of Fusarium proliferatum DSM106835 genome

Constructed a gapless reference genome of the UAE sudden decline syndrome pathogen F. proliferatum using long-read PacBio HiFi and Omni-C sequencing.

Genomics PacBio HiFi Omni-C IF: 7.2
View DOI
Research Project PhD Thesis Focus (2023)

Fusarium proliferatum Telomere-to-Telomere Scaffolding

Sequencing and scaffolding of the F. proliferatum genome using long-read ONT and physical contact maps (Omni-C) to produce a fully resolved, gapless reference genome.

Omni-C Nanopore Bioinformatics
Read Overview
Q1 Publication Frontiers in Plant Science (2022)

The 1-aminocyclopropane-1-carboxylic acid deaminase-producing Streptomyces violaceoruber UAE1 can provide protection from sudden decline syndrome on date palm

Evaluated Streptomyces violaceoruber UAE1 as a biocontrol agent against F. solani, demonstrating ACC deaminase-mediated reduction of stress hormone precursor levels.

Biocontrol ACC Deaminase Streptomyces IF: 5.6
View DOI
International Award 15th Session (2022)

Khalifa International Award for Date Palm and Agricultural Innovation

Distinguished Innovative Studies & Modern Technology Category recipient for biocontrol modeling of SDS pathogens using ACC deaminase-producing Streptomyces.

Biocontrol Innovation Agriculture
Award Website
Q1 Publication Journal of Fungi (2021)

Biocontrol potential of endophytic actinobacteria against Fusarium solani, the causal agent of sudden decline syndrome on date palm in the UAE

Isolated and characterized 31 endophytic actinobacterial strains from healthy date palm roots, identifying UAE1 and UAE2 as strong antagonists of F. solani via wall-degrading enzymes.

Endophytes Fusarium solani Date Palm IF: 4.7
View DOI
Publication Data in Brief (2020)

Data on large cardamom transcriptome associated with Chirke disease

Provided comparative RNA-seq transcriptome data from healthy and Chirke virus-infected cardamom plants, establishing a key genomic database for LCCV research.

Transcriptome Cardamom Chirke Virus IF: 1.2
View DOI
Academic Career

Experience & Academic Service

Chronology of research appointments, education, institutional administration, and professional service.

Research Associate (Postdoctoral)

2025 – Present

United Arab Emirates University (UAEU), Al Ain, Abu Dhabi, UAE

Leading research on functional genomics of plant-microbe interactions and developing Nextflow bioinformatics workflows under competitive Strategic Research Grant funding.

PhD in Cellular and Molecular Biology

2021 – 2025

United Arab Emirates University (UAEU), Al Ain, Abu Dhabi, UAE

Fully funded scholar focused on high-quality chromosome-level assemblies and transcriptome profiles of date palm pathogens. Supervised by Prof. Synan F. AbuQamar.

Research Assistant & Bioinformatician

2019 – 2021

JNTBGRI, Thiruvananthapuram, Keralam, India

Created computational pipelines for plant genomics. Administered and managed the institutional Galaxy Bioinformatics server with Anaconda integration.

MSc in Bioinformatics

2017 – 2019

Union Christian College, Ernakulam, India

Graduated with specialization in computational sequence analysis, genome organization, and molecular modeling paradigms.

Professional Service

  • Peer Reviewer: Scientific Data, Scientific Reports, BMC Genomics, BMC Plant Biology, Frontiers in Plant Science, Frontiers in Microbiology.
  • Teaching: TA for Basic Biology laboratories (4 semesters) & Instructor for Research Project course (6 semesters) at UAEU.
  • Organizations: Organizing committee for UAE Microbiome Conference (2023) and Gulf-4 International Conference (2024).

Technical Skill Registry

Genomics / Dry Lab

• RNA-Seq Analysis • Hi-C / Omni-C Assembly • Pan-genomics • Phylogenetics • Nextflow & Singularity • Python, R & Rust

Molecular / Wet Lab

• DNA/RNA Isolation • DNBSEQ & ONT Sequencing • qPCR & RT-qPCR • Bio-control Screenings • Plant Tissue Culture • Western Blotting
Design Sandbox
Accent Palette
Density Scaling