Hybrid Catfish (C. macrocephalus × C. gariepinus)

We report the haplotype-resolved genome assembly of a Thai hybrid catfish (F1), an allodiploid created by crossing two parent species.

Challenge & Solution:

• Challenge: High heterozygosity (>10%) causing fragmented assemblies
• Solution: Applied Hifiasm Hi-C and HapHiC algorithms to separate haplotypes

Results:

• Two phased, haploid-complete parental assemblies
• 27 chromosomes (C. macrocephalus) and 28 chromosomes (C. gariepinus)
• Total genome size: 1.8 Gb with 97% BUSCO completeness

NCBI BioProject: PRJNA115349 DOI: ANDRES, Q. L. S., Singchat, W., & Srikulnath, K. (2025). Dual Reference Genomes from F1 Hybrids: Phased Assembly of North African Catfish and Bighead Catfish with Hi-C Data. https://doi.org/10.5281/zenodo.14959133

Streptococcus iniae from Asian Seabass

Analysis of bacterial isolates from diseased farmed fish to understand pathogenicity and antimicrobial resistance patterns.

Methodologies:

• Reference-guided de novo assembly
• Full-length bacterial chromosome reconstruction
• Multi-reference mapping to pangenome graphs for AMR assessment
• Analysis of virulence factors and host adaptation

NCBI BioProject: PRJNA933632 DOI: ANDRES, Q. L. S. (2024). Comparative Genomics and Reverse Vaccinology of Streptococcus iniae from Thai Aquaculture Isolates: A Genomic Approach to Vaccine Development. Zenodo. https://doi.org/10.5281/zenodo.15264954

Bacterial Vaccine Development for Nile Tilapia

Developed vaccines against major pathogens affecting Tilapia aquaculture, including Streptococcus iniae and Aeromonas veronii.

Approaches:

• Inactivated whole-cell lipid coated vaccines with optimized adjuvants
• Validation through challenge studies and immune response profiling
• Assessment of cross-protection against heterologous strains

Results:

• Achieved >80% relative percent survival in laboratory trials
• Identified optimal administration routes and timing
• Developed practical formulations suitable for field application

DOI: ANDRES, Q. L. S. (2022). Heat-Killed Bivalent Vaccination in Nile Tilapia: A Low-Cost IMM+OR Protocol Protects Against Streptococcus agalactiae and Aeromonas veronii (v1.0). Zenodo. https://doi.org/10.5281/zenodo.15263492

Computational Vaccine Candidate Discovery

Applied genomics-driven reverse vaccinology to identify promising vaccine antigens from aquaculture pathogens.

Methodology:

• Comprehensive in silico prediction of surface-exposed proteins
• Multi-parameter antigen scoring for immunogenicity potential
• Structural modeling of candidate antigens
• Conservation analysis across strain collections
• Epitope mapping and MHC binding prediction

Key Findings:

• Identified SortaseA as a promising cross-protective antigen
• Mapped conserved B-cell and T-cell epitopes
• Developed recombinant expression systems for top candidates
• Validated immunogenicity through in vitro and in vivo studies

Bacterial Pangenome Analysis

Characterized core and accessory genome components of fish pathogens to understand population structure and virulence mechanisms.

Approaches:

• Graph-based pangenome construction using multiple reference genomes
• Classification of core, shell, and cloud genes
• Functional annotation of lineage-specific elements
• Identification of mobile genetic elements and horizontal gene transfer
• Correlation of gene presence/absence with virulence phenotypes

Applications:

• Identified molecular determinants of host specificity
• Tracked evolution of antimicrobial resistance
• Characterized strain-specific virulence factors
• Developed diagnostic markers for pathotype identification

Genome & Transcriptome Analysis

• Assembly: HifiAsm, Flye, Canu, SPAdes, Unicycler
• Quality Assessment: QUAST, BUSCO, Merqury, FastANI
• Annotation: Prokka, PGAP, MAKER
• Alignments: Miniprot, Bowtie2, BWA, BWA-MEM, Minimap2, Winnowmap, VerityMap, VG Giraffe
• Comparative Genomics: IGV, Mauve, Roary, OrthoFinder, PAML
• Variant Calling & Rare-Disease Interpretation:
  • Small variants & polishing – GATK (HaplotypeCaller), DeepVariant, FreeBayes, Clair3, Pilon
  • Structural variants – bcftools/vcftools, JasmineSV
  • Data handling & QC – Picard, Truvari
  • Functional annotation – SnpEff, Ensembl VEP
  • Clinical databases – ClinVar / ClinGen
• Transcriptome / RNA-seq: HISAT2, STAR, Salmon, Kallisto, Trinity (de novo assembly), RSEM, HTSeq, featureCounts, DESeq2, edgeR

Programming & Analysis

• R (⭐⭐⭐⭐⭐) - Statistical analysis, data visualization, genomic data processing
• Bash/Linux (⭐⭐⭐⭐⭐) - Pipeline automation, HPC job management
• Python (⭐⭐⭐⭐) - Bioinformatics tool development, data processing
• Perl (⭐⭐⭐) - Legacy bioinformatics scripts
• C# (⭐⭐⭐) - Unity prototyping, editor tooling
• HPC / SLURM / Docker / Singularity / Mamba / Bioconda (⭐⭐⭐⭐⭐) - Scalable workflows, containerization, reproducible environments