Phylogenetic Implication of Large Intergenic Spacers: Insights from a Mitogenomic Comparison of Prosopocoilus Stag Beetles (Coleoptera: Lucanidae)

Abstract

To explore the characteristics of mitogenomes and discuss the phylogenetic relationships within the genus Prosopocoilus, the mitogenomes of two species (P. castaneus and P. laterotarsus) were newly sequenced and comparatively analyzed. The arrangement of the mitogenome in these two lucanid beetles was the same as that in the inferred ancestral insect, and the nucleotide composition was highly biased towards A + T as in other lucanids. The evolutionary rates of 13 protein-coding genes (PCGs) suggested that their evolution was based on purifying selection. Notably, we found evidence of the presence of a large IGS between trnI and trnQ genes, whose length varied from 375 bp (in P. castaneus) to 158 bp (in P. laterotarsus). Within the large IGS region, a short sequence (TAAAA) was found to be unique among these two species, providing insights into phylogenomic reconstruction. Phylogenetic analyses were performed using the maximum likelihood (IQ-TREE) and Bayesian (PhyloBayes) methods based on 13 protein-coding genes (PCGs) in nucleotides and amino acids (AA) from published mitogenomes (n = 29). The genus Prosopocoilus was found to constitute a distinct clade with high nodal support. Overall, our findings suggested that analysis of the characteristics of the large IGS (presence or absence, size, and location) in mitogenomes of the genus Prosopocoilus may be informative for the phylogenetic and taxonomic analyses and for evaluation of the genus Prosopocoilus, despite the dense sampling materials needed.

The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes

“…The long IGS of Batocera sp., a 1428 bp spacer with 17 repeat fragments and high AT content, is between trnW and trnC (note: these are usually characteristic of the A+T-rich region) (Figure 3, Table S19). Similar structures have been found in Pyrocoelia rufa [74], Evania appendigaster [94], and Metopodontus blanchardi [103,104] (Table S20).…”

“…In the studies of Bae et al [74], Wei et al [94], and Kim et al [104], the authors did not offer an explanation for how this IGS was formed or what its function was. Xu et al also performed an analysis of large IGS in the genus Prosopocoilus (Lucanidae) [103] and discovered IGSs between trnI and trnQ in the mitochondrial genome of genus Prosopocoilus (Lucanidae), with varying lengths from 375 bp to 4051 bp [103]. Such IGSs have only been found in the mitochondrial genomes of this genus.…”

Utilisation of a mitochondrial intergenic region for species differentiation of fruit flies (Diptera: Tephritidae) in South Africa

“…Notably in this study, the size of the intergenic region I is relatively consistent within species and significantly different between species to allow for unambiguous differentiation of these five fruit fly species. Species identification based on the size of mitochondrial intergenic regions has shown to be successful in a wide range of bacteria and is emerging in insect phylogenetics [33,[51][52][53][54]. It is important to frame this work in a greater context of mitochondrial datasets being at the forefront of the exploration of evolutionary relationships.…”

The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia

“…This conserved gene order allows for the identification and comparison of homologous genes, aiding in the alignment and analysis of mitogenomic sequences. Various biologists analyzed the mitogenome data set through bayesian inferences (BI) and maximum likelihood (ML) methods and evaluated as a powerful tool to reconstruct the phylogenetic relationship among insects [ 39 , 40 ]. IB analysis provides a statically robust framework to estimate evolutionary relationships.…”