Haplotype-Resolved Chromosome-scale Assembly of the Bighead Catfish (Clarias macrocephalus) Genome

Haplotype-Resolved Chromosome-Scale Genome Assembly of the Thai Bighead Catfish (Clarias macrocephalus)

This study presents the first high-quality, chromosome-scale, haplotype-resolved genome assembly of the Bighead catfish (Clarias macrocephalus), a freshwater species native to Thailand and the Mekong River basin. As a species of economic and ecological importance, C. macrocephalus plays a key role in Southeast Asian aquaculture and conservation efforts.

The assembly was generated using a combination of third-generation sequencing technologies, including PacBio HiFi, Oxford Nanopore (ONT), Hi-C, and Illumina paired-end sequencing. The resulting haplotype-resolved diploid genome spans 880 Mb across 27 pseudo-chromosomes, exhibiting high contiguity (N50 = 35.4 Mb), completeness (BUSCO = 95.5%, K-mers-Merqury-k21 = 96,6%), and base-level accuracy (QV50, corresponding to 99.999% correctness). The genome was manually curated and scaffolded using Hi-C chromatin conformation capture data, providing a comprehensive reference for future research.

This assembly fills a critical gap in genomic resources for the Clarias genus, offering valuable insights into structural variations, genetic diversity, and the effects of selective breeding of C. macrocephalus. The dataset supports applications in comparative genomics, conservation, aquaculture breeding programs, and pan-genome graph construction. Furthermore, it enables research into adaptive traits, such as the species’ benthic lifestyle and facultative air-breathing capability, which allow survival in low-oxygen environments.

Aligned with the United Nations’ Sustainable Development Goal (SDG) 2 (Zero Hunger), this genomic resource contributes to sustainable aquaculture and biodiversity conservation. All sequencing data, genome assemblies, and computational workflows are publicly available under NCBI BioProject number PRJNA1121957, supporting further research in fish genomics, hybridization studies, and genome evolution. All datasets and computational workflows are openly accessible to support further research in fish genomics and hybrid genome analysis.

📂 Data Records

🐟 Genome Assembly of Thai Bighead Catfish (isolate: CMAM) – Bighead catfish (TaxID: 35657)

📜 Raw Sequenced Reads (NCBI SRA)
🔬 Nanopore (20% err.): 🔗 SRR29723575 (SRR29723575)  
🧪 HiFi: 🔗 SRR29723576 (SRR29723576)  
🖥️ Illumina 150PE: 🔗 SRR29723578 (SRR29723578)  
🧲 Hi-C 150PE: 🔗 SRR29723577 (SRR29723577)  

🗂️ The assembled genome, deposited as a whole-genome sequence (WGS) diploid assembly. 

🐠 Haplotype 1 | 🐟 Haplotype 2.

🧬 GenBank accession numbers: 🔗 JBLWMO000000000 (JBLWMO000000000) | 🔗 JBLWMP000000000 (JBLWMP000000000).  

DATA DESCRIPTION (Final Assemblies (usable):

📌 Data records are hosted under NCBI BioProject number: 🔗 PRJNA1132508 (WGS), PRJNA1159889 (Hap1), PRJNA1159890 (Hap2) 
📌 Bighead Catfish BioSample accession number: 🔗 SAMN42347118 (SAMN42347118)  

Other assemblies (Intermediate Files):