Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae)

Abstract

The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.

Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae

“…The loss of the DHU arm in tRNAs has been detected in various Lepidoptera species [ 6 , 38 , 39 ]. DHU lacking arm was hypothesized to have evolved in response to recognition signals for seryl-tRNA synthetases, reflecting potential differences in gene expression [ 40 , 41 ]. The location of rrnL is between trnV and trnL1 , while rrnS is detected between the control region and trnV .…”

Phylomitogenomics reveals mito‐nuclear concordance in social wasps: The performance of mitochondrial markers and gene order for hymenopteran systematics

“…Even within the genomics era, mtDNA data remain a useful and cost‐efficient molecular marker, especially for preliminary species delimitation and identification, and for estimating levels of population structure, gene flow, and demographic history. The sequencing of complete insect mitogenomes has become more frequent (Bessa et al, 2021; X. Feng et al, 2022; Ruiz‐Mena et al, 2022; Tang et al, 2019; Yamasaki et al, 2020; Q. H. Zhang, Huang, et al, 2018; C. Zhang, Rabiee, et al, 2018) but comparative studies testing the phylogenetic utility of mitogenomes as a whole (Wei et al, 2010) or the relative performance of different mtDNA genes are scarce for invertebrate groups in general (for few exceptions, see Havird & Santos, 2014; Seixas et al, 2016; Talavera & Vila, 2011). This is problematic because a better understanding of mtDNA properties is essential for the application of mtDNA for molecular systematics (Dong et al, 2021).…”

“…Even within the genomics era, mtDNA data remain a useful and cost-efficient molecular marker, especially for preliminary species delimitation and identification, and for estimating levels of population structure, gene flow, and demographic history. The sequencing of complete insect mitogenomes has become more frequent (Bessa et al, 2021;X. Feng et al, 2022;Ruiz-Mena et al, 2022;Tang et al, 2019;Yamasaki et al, 2020;Q.…”