Beyond the Beauty: Meristic and Genomic Signatures of Bangka’s Endemic Betta Fishes

<ns7:p> Background The genus <ns7:italic>Betta</ns7:italic> (family Osphronemidae) comprises over 70 species, many of which are endemic to Southeast Asia and highly vulnerable to habitat loss. While <ns7:italic>Betta splendens</ns7:italic> is well studied due to its importance in the ornamental fish trade, most wild <ns7:italic>Betta</ns7:italic> species remain poorly characterized, particularly at the genomic level. The Bangka Islands of Indonesia harbor several endemic <ns7:italic>Betta</ns7:italic> species threatened by peatland degradation. Methods We conducted an integrated meristic and genomic comparison of three endemic Bangka Island species— <ns7:italic>Betta burdigala</ns7:italic> , <ns7:italic>B. chloropharynx</ns7:italic> , and <ns7:italic>B. schalleri.</ns7:italic> Specimens were collected from peatland waters in Bangka, and meristic traits were examined to confirm diagnostic characteristics. High-molecular-weight DNA was extracted and sequenced using Oxford Nanopore PromethION technology, followed by <ns7:italic>de novo</ns7:italic> assembly and reference-guided scaffolding using the <ns7:italic>Betta splendens</ns7:italic> genome. Results The meristic analysis confirmed features consistent with their taxonomic placement within the <ns7:italic>coccina</ns7:italic> , <ns7:italic>waseri</ns7:italic> , and <ns7:italic>pugnax</ns7:italic> groups. Genome assembljies were highly contiguous and complete (BUSCO &gt;97%), with <ns7:italic>B. chloropharynx</ns7:italic> showing the largest genome size, highest scaffold N50, and elevated retrotransposon content. Gene duplication analysis revealed dispersed duplications as the dominant category across all genomes, with variation in tandem and proximal duplicates. Comparative genomic analysis demonstrated high collinearity, with <ns7:italic>B. chloropharynx</ns7:italic> and <ns7:italic>B. schalleri</ns7:italic> showing the closest relationship, while <ns7:italic>B. burdigala</ns7:italic> diverged earlier. The Colony Stimulating Factor 1 Receptor A (CSF1RA) protein phylogenetic tree closely resembles the phylogenetic tree of nine fish species based on NCBI taxonomic data. We also identified two massive protein insertions in the CSF1RA of <ns7:italic>B. burdigala.</ns7:italic> Conclusions This study provides morphological and genomic evidence supporting the distinctiveness of Bangka’s endemic <ns7:italic>Betta</ns7:italic> species and delivers essential genomic resources for evolutionary research and conservation of these endangered freshwater fishes. </ns7:p>