Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability

Abstract

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143–16,803 bp and 15,933–16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica.

Phylogenetic insights based on the first complete mitochondrial genome of Isomyia nebulosa (Diptera: Calliphoridae)

“…Twelve PCGs share start codon ATD (ATA for ND1 ; ATG for ATP6 , COX2 , COX3 , CYTB , ND4 , and ND4L ; ATT for ATP8 , ND2 , ND3 , ND5 , and ND6 ), whereas COX1 starts with TCG as other dipteran species (Huang and Ma 2018 ; Zhang et al. 2023 ). All PCGs terminate with either TAY (TAA for ATP6 , ATP8 , COX2 , COX3 , CYTB , ND2 , ND3 , ND4L , and ND6 ; TAG for ND1 ) or incomplete stop codon T ( COX1 , ND4 , and ND5 ).…”

“…The mitogenome of I. nebulosa was assembled from the raw sequencing data (NCBI Short Read Archive, SRA accession number SRR25915118) using Geneious Prime v2023.0.4 and annotated following the study of Zhang et al. ( 2023 ) except for using the mitogenome of Polleniopsis mongolica Séguy, 1928 (MT017721) (Shang et al. 2022 ) as a reference.…”

“…The nucleotide sequences of concatenated 13 protein-coding genes (PCGs) and two rRNAs of the 23 mitogenomes were aligned, partitioned, analyzed, and visualized following the methods in Zhang et al. ( 2023 ). Briefly, we used PartitionFinder v2.1 (Lanfear et al 2017 ) for selecting best-fit partitioning schemes and models, and used MrBayes v3.2.7a (Ronquist et al.…”