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. 2023 Apr 8;14(4):883.
doi: 10.3390/genes14040883.

Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

Shenghui Bi  1   2 , Yanfei Song  2 , Linggao Liu  1 , Jing Wan  1 , Ying Zhou  1 , Qiujin Zhu  1 , Jianfeng Liu  2
Affiliations

Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

Shenghui Bi et al. Genes (Basel). .

Abstract

Piophila casei is a flesh-feeding Diptera insect that adversely affects foodstuffs, such as dry-cured ham and cheese, and decaying human and animal carcasses. However, the unknown mitochondrial genome of P. casei can provide information on its genetic structure and phylogenetic position, which is of great significance to the research on its prevention and control. Therefore, we sequenced, annotated, and analyzed the previously unknown complete mitochondrial genome of P. casei. The complete mt genome of P. casei is a typical circular DNA, 15,785 bp in length, with a high A + T content of 76.6%. It contains 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region. Phylogenetic analysis of 25 Diptera species was conducted using Bayesian and maximum likelihood methods, and their divergence times were inferred. The comparison of the mt genomes from two morphologically similar insects P. casei and Piophila megastigmata indicates a divergence time of 7.28 MYA between these species. The study provides a reference for understanding the forensic medicine, taxonomy, and genetics of P. casei.

Keywords: Piophilidae; comparative analyses; mitochondrial DNA; phylogenetic analysis.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
The mt genome of eight species. (a) P. casei, (b) P. megastigmata, (c) B. dorsalis, (d) Z. caudatus, (e) L. bryoniae, (f) A. oryzalimnetes, (g) H. interstincta, and (h) T. scita. The chain is marked with an arrow indicating the direction of gene transcription. Gene lengths correspond to nucleotide lengths in the diagram. The outermost layer is the J chain, and the second layer is the N chain. The third black peak indicates GC content, and the purple and green peaks indicate the ±skew of GC.
Figure 2
Figure 2
AT content of genes in various parts of the mt genome among the nine species in Tephritoidea.
Figure 3
Figure 3
(a) Nucleotide diversity (Pi) values of P. casei and P. megastigmata PCGs; (b) Pi values and Ka/Ks values of PCGs in the mt genomes of 26 species.
Figure 4
Figure 4
RSCU information of PCGs (a) Relative synonymous codon usage (RSCU) in the mtgenomes of P. casei; (b) ENc-plot of P. casei; (c) Amino acid usage graph for P. casei; (d) Heat map of RSCU results for P. casei calculated by CodonW software; (e) Relative synonymous codon usage (RSCU) in the mtgenomes of P. megastigmata; (f) ENc-plot of P. megastigmata; (g) Amino acid usage graph for P. megastigmata; (h) Heat map of RSCU results for P. megastigmata calculated by CodonW software.
Figure 5
Figure 5
The 22 tRNA secondary structures of P. casei. The numbers below indicate their sequence position in the mt genome.
Figure 6
Figure 6
Secondary structure of rrnS and rrnL mt genome of P. casei.
Figure 7
Figure 7
Substitution saturation plots of mt genomic PCGs and RNAs for 26 species. Plots in blue and green indicate transition and transversion, respectively.
Figure 8
Figure 8
A genome-wide phylogenetic tree of the mitochondria of 26 dipteran insect species constructed based on ML analysis. Two values of developmental dendrites (SH-aLRT support/bootstrap support). (The specie marked with ** is the main subjects of study in this research).
Figure 9
Figure 9
A genome-wide phylogenetic tree of the mitochondria of 26 dipteran insect species constructed based on BI analysis. The red values in the developmental tree indicate the time of divergence between species MYA (million years ago). (The specie marked with ** is the main subjects of study in this research).
See this image and copyright information in PMC

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