Chromosome-level genome assembly and annotation of the male Andinoacara rivulatus
TL;DR
This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of male Andinoacara rivulatus, with direct implications for sustainable aquaculture and the global ornamental fish trade.
Abstract
The family Cichlidae, exemplified by Andinoacara rivulatus , is a widely recognized model system for studying adaptive radiation and phenotypic diversity in freshwater fishes. Furthermore, A. rivulatus is an important ornamental fish species exhibiting significant sexual dimorphism, monosex fish breeding and has important application prospects for aquaculture. Here, we present the first high-contiguity chromosome-level genome assembly of male A. rivulatus , constructed using a multi-platform approach combining PacBio HiFi long-read sequencing, MGI paired-end short reads, and Hi-C data. The assembly spans 778.79 Mb with a contig N50 of 27.16 Mb and scaffold N50 of 32.80 Mb, anchored to 24 chromosomes (99.33% anchoring rate). Repeat annotation revealed that 32.60% of the genome consists of repetitive elements, including 20.51% known transposable elements. We predicted 24,838 protein-coding genes with an average of 10.22 exons per gene, and functional annotation identified evolutionarily conserved domains and key metabolic pathways. BUSCO assessment demonstrated 99.23% completeness, confirming the assembly’s high quality. This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of A. rivulatus , with direct implications for sustainable aquaculture and the global ornamental fish trade.