Long-read Sequencing Data Reveals Dynamic Evolution of Mitochondrial Genome Size and the Phylogenetic Utility of Mitochondrial DNA in Hercules Beetles (Dynastes; Scarabaeidae)

Abstract

The evolutionary dynamics and phylogenetic utility of mitochondrial genomes (mitogenomes) have been of particular interest to systematists and evolutionary biologists. However, certain mitochondrial features, such as the molecular evolution of the control region in insects, remain poorly explored due to technological constraints. Using a combination of long- and short-read sequencing data, we assembled ten complete mitogenomes from ten Hercules beetles. We found large-sized mitogenomes (from 24 to 28 kb), which are among the largest in insects. The variation in genome size can be attributed to copy-number evolution of tandem repeats in the control region. Furthermore, one type of tandem repeat was found flanking the conserved sequence block in the control region. Importantly, such variation, which made up around 30% of the size of the mitogenome, may only become detectable should long-read sequencing technology be applied. We also found that, although different mitochondrial loci often inferred different phylogenetic histories, none of the mitochondrial loci statistically reject a concatenated mitochondrial phylogeny, supporting the hypothesis that all mitochondrial loci share a single genealogical history. We on the other hand reported statistical support for mito-nuclear phylogenetic discordance in 50% of mitochondrial loci. We argue that long-read DNA sequencing should become a standard application in the rapidly growing field of mitogenome sequencing. Furthermore, mitochondrial gene trees may differ even though they share a common genealogical history, and ND loci could be better candidates for phylogenetics than the commonly used COX1.

First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae)

“…The number, distribution, order, and orientation of genes were the same as those found in previously sequenced scarabs. AT skew and GC skew were similar to those of previous studies ( Yang et al 2019 , Choi et al 2020 , Morgan et al 2022 ). This study provides basic data on the phylogenetic development of Scarabaeidae.…”

Evolution of myxozoan mitochondrial genomes: insights from myxobolids

“…This characteristic was found also in the sister clade of Myxozoa, P. hydriforme [ 3 ]. While the mt genome of most animals is very compact and contains only short noncoding regions, long-read sequencing enabled the discovery of several similar cases of mt tandem repeats in both parasitic and non-parasitic animals, e.g., parasites: the parasitoid wasp Nasonia vitripennis [ 37 ], the cestode Echinococcus granulosus [ 38 ], the fluke Shistosoma haematobium [ 39 ]; free-living species: beetles of genus Dynastes [ 40 ], the stink bug Erthesina fullo [ 41 ], and frogs of genus Breviceps [ 42 ]. Further research is needed to elucidate how these regions are formed and whether there are any selective forces preventing them from being deleted.…”

The Water‐Exclusion Trap (WET): A 3D printable window trap collector that prevents DNA degradation

“…The DNA integrity of samples will be increasingly important with the wider use of long‐read sequencing technologies that require higher DNA integrity and high molecular weight DNA (Jones et al, 2021; Marx, 2023; Russo et al, 2022). These techniques have been used in various initiatives to sequence whole genomes (Hotaling et al, 2021), but are slowly becoming a standard of genetic analyses for entomology, as they are increasingly used in systematics, population genomics and biomonitoring (Krehenwinkel et al, 2019; Morgan et al, 2022). We need to move beyond sequencing a small number of model organisms that are readily available in the laboratory or must be immediately processed in the field, and suitable approaches must work for a wide variety of insects from different parts of the world.…”