Unraveling an extreme AT-rich and complex mitochondrial genome: the first complete mitogenome of the species-rich family Diaspididae (Hemiptera, Coccomorpha) and its evolutionary implications

TL;DR

This study reports the first complete mitochondrial genome of a scale insect, revealing extreme AT richness and structural complexity, offering insights into genome evolution and assembly methods.

Contribution

The study introduces a hybrid sequencing pipeline for assembling highly AT-rich and complex mitogenomes, resolving challenges in the species-rich Diaspididae family.

Findings

The A. yasumatsui mitogenome is the longest among scale insects at 21,273 bp with a 92% AT content.

It features extensive gene rearrangements, missing tRNA genes, and an ultra-long (>5,000 bp) repeat region.

Oxford Nanopore sequencing effectively mitigates coverage bias in Illumina data for such complex genomes.

Abstract

The assembly of insect mitochondrial genomes remains challenging in certain taxa due to extreme AT biases and long repetitive regions. The family Diaspididae (Hemiptera: Coccomorpha) exemplifies this difficulty; despite more than 2,700 described species worldwide, no complete mitogenome has been reported prior to this study. Here, the complete mitogenome is presented of Aulacaspis
yasumatsui, assembled using a hybrid approach combining second- and third-generation sequencing platforms. The A.
yasumatsui mitogenome is the longest identified to date among scale insects, spanning 21,273 bp. It exhibits several extraordinary features, most notably the highest AT content (92%) yet recorded in Insecta, extensive gene rearrangements, the absence of half of the tRNA genes, and the first identified ultra-long repeat region (> 5,000 bp) in Coccomorpha. The leg degeneration and loss observed in Diaspididae evolution may have contributed to the emergence of such an extreme mitogenome structure. Comparative analysis of sequencing strategies revealed substantial coverage bias in Illumina data, which was effectively mitigated by Oxford Nanopore long reads. We propose a standardized pipeline tailored for efficient and accurate assembly of highly AT-rich and structurally complex mitogenomes. This study provides both methodological insights and a valuable genomic resource for future evolutionary and comparative studies on Diaspididae and other taxa with challenging mitogenomes.

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