Resumo em Inglês:

Abstract Polyneoptera comprises hemimetabolous insect orders of significant agricultural, ecological, and medical relevance, motivating phylogenetic and molecular research that has nevertheless focused predominantly on canonical mitochondrial markers. Here, we assembled new mitogenomes for Polyneoptera and evaluated the usefulness of genes located in nucleotide-diversity hotspots as markers for species identification and phylogenetic inference. To expand the available mitogenomic resources, raw sequencing data were retrieved from public databases, resulting in the assembly and annotation of 26 complete mitogenomes, all exhibiting the typical insect mitochondrial architecture. These newly assembled genomes were combined with publicly available mitogenomes from Orthoptera, Blattodea, Plecoptera, Mantodea, and Phasmatodea to reconstruct phylogenetic relationships using both complete and reduced datasets comprising nucleotide-diversity hotspot-associated genes. The performance of these hotspot regions was further assessed through barcoding gap analyses and comparisons with the most comprehensive datasets to identify candidate mitochondrial markers for molecular species identification and phylogenetic inference. Across orders, different mitochondrial regions, including the classical markers 16S and COX1, as well as genes from the NADH dehydrogenase complex, emerged as the most informative, although optimal markers varied among lineages. Overall, our findings highlight the value of publicly accessible sequencing data for generating high-quality genomic resources and improving phylogenetic and taxonomic tools.

Resumo em Inglês:

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.