Dual Reference Genomes from F1 Hybrids: Phased Assembly of North African Catfish and Bighead Catfish with Hi-C Data
Year: 2025
Type: article
Abstract: Dual Reference Genomes from F1 Hybrids: Phased Assembly of North African Catfish and Bighead Catfish with Hi-C Data This study presents high-quality, phased genome assemblies for the North African catfish (Clarias gariepinus) and Bighead catfish (Clarias macrocephalus) using an F1 hybrid individual. By integrating Hi-C chromatin conformation capture data, we generated two haplotype-resolved reference genomes, providing valuable genomic insights into hybridization, adaptation, and aquaculture genetics. The assemblies offer a crucial resource for comparative genomics, evolutionary studies, and breeding programs, and are particularily relevant for Thailand and Mekong aquaculture. All datasets and computational workflows are openly accessible to support further research in fish genomics and hybrid genome analysis. 📂 Data Records 🐟 Genome Assembly of F1 Hybrid Catfish (isolate: CGAF) – Bighead catfish (TaxID: 35657) and North African catfish (TaxID: 13013) subgenomes. 🧬 GenBank accession numbers: 🔗 JBLWFY000000000 (JBLWFY000000000.1) | 🔗 JBLWFZ000000000 (JBLWFZ000000000.1). 📌 Data records are hosted under NCBI BioProject number: 🔗 PRJNA1153495 (PRJNA1153495) 📌 F1 hybrid catfish (TaxID: 1334085) BioSample accession number: 🔗 SAMN43395848 (SAMN43395848) 📜 Raw Sequenced Reads (NCBI SRA)🔬 Nanopore (20% err.): 🔗 SRR30599638 (SRR30599638) 🧪 HiFi: 🔗 SRR30599641 (SRR30599641) 🖥️ Illumina 150PE: 🔗 SRR30599640 (SRR30599640) 🧲 Hi-C 150PE: 🔗 SRR30599639 (SRR30599639) 🗂️ The assembled genome, deposited as a whole-genome sequence (WGS) diploid assembly, designates parental samples: - 🐠 Haplotype 1: C. macrocephalus - 🐟 Haplotype 2 (C. gariepinus BioSample accession numbers): - 🔗 SAMN46907808 (SAMN46907808) - 🔗 SAMN46730924 (SAMN46730924) 📜 Additional Illumina Non-Hi-C Sequencing Data- 👩🔬 Female C. macrocephalus: 🔗 SAMN42503781 (SAMN42503781) - 👨🔬 Male C. gariepinus: 🔗 SAMN43548335 (SAMN43548335) DATA DESCRIPTION (ZENODO): Step Description Tool Library Type Assembly File Name (Output) File Name Suffix (Output) Final Assemblies (usable) LATEST VERSION (v19+) Haplotype 1 - Bighead catfish (TaxID: 35657) Hifiasm + HapHic + JBAT+TGS-GapCloser + Polishing + Manual Curation (round 19+) HiC + UL + HiFi + PE150 Fully phased manually reviewed polished haplotype 1 Hybrid_catfish_polished_19.fa fClaHyb_Mac*.fa LATEST VERSION (v19+) Haplotype 2 - North African catfish (TaxID: 13013) Hifiasm + HapHic + JBAT+TGS-GapCloser + Polishing + Manual Curation (round 19+) HiC + UL + HiFi + PE150 Fully phased manually reviewed polished haplotype 2 Hybrid_catfish_polished_19.fa fClaHyb_Gar*.fa NCBI (usable) Version 1 NCBI-Submitted Haplotype 1 - Bighead catfish (TaxID: 35657) Hifiasm + HapHic+ JBAT+TGS-GapCloser + Polishing + Manual Curation HiC + UL + HiFi + PE150 Fully phased manually reviewed polished haplotype 1 🔗 JBLWFY000000000 (JBLWFY000000000.1) .fa Version 1 NCBI-Submitted Haplotype 2 - North African catfish (TaxID: 13013) Hifiasm + HapHic + JBAT+TGS-GapCloser + Polishing + Manual Curation HiC + UL + HiFi + PE150 Fully phased manually reviewed polished haplotype 2 🔗 JBLWFZ000000000 (JBLWFZ000000000.1) .fa ADDITIONAL (usable) Flye Contigs Collapsed Assembly Flye (10 rounds of minimap2) HiFi Collapsed diploid assembly CGAF_Flye.assembly.fasta .assembly.fa GreenHill Scaffolds Haplotype-resolved assembly Hifiasm + GreenHiill HiC + UL + HiFi + PE150 Fully phased haplotype 1 and 2 consensus assembly out_afterPhase.fa .fa GreenHill Scaffolds Haplotype-resolved assembly Hifiasm + GreenHiill HiC + UL + HiFi + PE150 Fully phased haplotype 1 and 2 consensus assembly out_ConsensusOutput.fa .fa Hifiasm Polished unitigs Haplotype-resolved assembly Hifiasm HiC + UL + HiFi Fully phased haplotype 1 and 2 haplotype resolved assembly CGA_HIC_UL.asm.hic.p_utg.fa .fa
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6930625948
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