Comparative mitogenomics of six Thrips species reveals conserved architecture, repeat variation, and nucleotide composition bias.

Abstract

Thrips are widely distributed insects with economic importance, but their evolutionary dynamics of the mitochondrial genome remain poorly understood. This study presented a computational mitogenomic analysis of six Thrips species obtained from a public repository. An analysis was performed to investigate patterns of genomic architecture and evolutionary variations. Mitochondrial genomes were analyzed using bioinformatic approaches, including annotation, syntenic comparison, gene content analysis, and SSR identification. Codon usage bias was measured using RSCU and CAI metrics, while skewness in nucleotide composition was studied using AT and GC skew analyses. Results suggest that there is generally a conservation of mitochondrial genome organization among the different species, but only limited rearrangements occur, and these are mainly associated with tRNA and non-coding sequences. The presence or absence of genes in Thrips was verified by re-annotation with MITOS2, followed by confirmation in the feature table in GenBank. SSR analysis showed few notable interspecific variability, where T. palmi and T. hawaiiensis seemed to have higher motif diversity and density, sort of. Codon usage patterns looked like they had a strong bias towards A/T-ending codons, and the CAI values suggested different levels of codon usage adaptation across species, using reference sets that were built from the mitochondrial protein-coding genes themselves. Also, we consistently observed positive AT-skew and negative GC-skew across all genomes, with more pronounced asymmetry in T. palmi and T. hawaiiensis. Overall, this work points to both conserved traits and lineage-specific features in Thrips mitochondrial genomes, giving some clues about their evolutionary dynamics while also broadening our understanding of insect mitochondrial genome evolution.