Complete mitochondrial genomes of three Cichla species: annotation, diversity, and phylogenetic insights

Abstract

The Cichlidae family, especially the South American genus Cichla, is notable for its rapid diversification and ecological impacts following introductions outside its native range. In this study, we first describe the mitogenomes of three Cichla species. The mitogenome of Cichla piquiti was sequenced from a sample collected at Serra da Mesa Lake, located in the state of Goiás, Brazil. Additionally, the mitogenomes of Cichla monoculus and Cichla temensis were assembled using public data. The mitogenomes were assembled using NovoPlasty, and comparative analyses were performed, including those of the Cichla ocellaris mitogenome data. The mitogenomes ranged from 16,526 bp (C. monoculus) to 16,536 bp (C. piquiti), exhibiting a conserved genomic structure with 13 protein-coding genes, 22 tRNAs, and two rRNAs. These mitogenomes were validated by reconstructing phylogenetic relationships within the Cichlinae subfamily. We identified nucleotide composition biases and observed high nucleotide diversity in the D-loop region. Phylogenetic analysis based on complete mitogenome data indicated that Cichla species form a clade with C. ocellaris, a sister clade to Retroculini. This study provides new mitogenomic insights into Cichla, offering valuable genomic resources for species identification and ecological monitoring.