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

Abstract

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.