Reference-guided draft genome assembly of the slender walking catfish, Prophagorus nieuhofii

The slender walking catfish, Prophagorus nieuhofii, plays an important role in small-scale fisheries across Southeast Asia, supporting food security. While IUCN currently lists it as a Least Concern species, growing demand and pressures such as overfishing, habitat loss, and degradation may elevate its conservation risk. To support sustainable fisheries management and aquaculture, we sequenced, assembled, and annotated the whole genome of this species. The specimen was part of an expedition to document and preserve the genetic resources of aquatic animals in Kalimantan’s freshwater ecosystems. Using 27 Gb of sequence data, we assembled a 1.1 Gb genome comprising 5,790 scaffolds. This genome assembly has high contiguity and completeness, with N50 of 33.7 Mb and a BUSCO score of 98.8%. Repeat annotation revealed that 48.17% of the genome consisted of repetitive elements, predominantly DNA transposons (18.56%) and retroelements (13.30%). Structural annotation identified 30,099 protein-coding genes and 37,734 transcripts, most of which were multi-exonic and rich in alternative splicing. BUSCO analysis confirmed the high completeness of the genome and annotation, with 97.7% of the conserved orthologs being detected.

• Publication year

  2025

• Venue

  F1000Research

• Publication date

  2025-11-10

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.12688/f1000research.166849.2PMID 41458394PMCID 12743208
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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