Maccullochella peelii peelii Genome Decodes Insights into Its Genomic Characteristics and Population Dynamics

Maccullochella peelii peelii, the largest endemic freshwater fish in Australia, is a valuable species with considerable aquaculture potential. Despite its ecological and economic importance, its genome and phylogenetic history have been poorly studied due to a lack of genomic resources. In this study, we present the first comprehensive whole-genome survey and de novo assembly of M. peelii peelii. K-mer distribution analysis estimated the genome size to be 744.31 Mb, with a heterozygosity of 0.18% and a repetitive sequence content of 42.22%. The final assembled genome size reached a size of 731.74 Mb, and the assembly completeness was assessed by BUSCO, and the resulting score was 87.88%. The mitochondrial genome spans 16,422 bp, with a GC content of 42.05%, and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis, based on orthologous single-copy genes and conserved mitochondrial genes, places M. peelii peelii within a monophyletic clade, in strong agreement with traditional morphological classifications. PSMC analysis reveals significant fluctuations in effective population size over the past million years, including a sharp bottleneck around 400 Kya, followed by recovery during the Last Interglacial Period (~130–116 Kya), likely driven by habitat improvements. These findings provide a critical genomic resource to address reproductive bottlenecks and enhance molecular breeding programs for this species.