The complete mitochondrial genome of the flesh fly, Muscina stabulans (Diptera: muscidae)

Application of omics techniques in forensic entomology research

With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field.

Phylogeny and Evolutionary Timescale of Muscidae (Diptera: Calyptratae) Inferred from Mitochondrial Genomes

House flies (Muscidae) comprise the most species-rich family of the muscoid grade with over 5000 described species worldwide, and they are abundant in various terrestrial and aquatic ecosystems. The high number of species, varied appearances, complex feeding habits, and wide distributions have hindered researchers from understanding their phylogeny and evolutionary history. Here, we newly sequenced fifteen mitochondrial genomes and reconstructed the phylogenetic relationships and divergence time among eight subfamilies of Muscidae (Diptera). The best phylogenetic tree, which was inferred by IQ-Tree, recovered the monophyly for seven out of eight subfamilies (except for Mydaeinae). Based on phylogenetic analyses and morphological characteristics, we prefer the subfamily status of Azeliinae and Reinwardtiinae, and separate Stomoxyinae from Muscinae. Genus Helina Robineau-Desvoidy, 1830 was synonymized with Phaonia Robineau-Desvoidy, 1830. The divergence time estimation indicated Muscidae originated at 51.59 Ma (early Eocene). Most subfamilies had originated around 41 Ma. We provided a mtgenomic viewpoint on the phylogenetic relationships and divergence time estimation of Muscidae.

The complete mitochondrial genome of the bazaar fly, Musca sorbens Wiedemann (Diptera: Muscidae)

The bazaar fly, Musca sorbens (Diptera: Muscidae) Wiedemann, 1830 is a world-wide species with sanitary, medical, and veterinary importance. The complete mitochondrial genome of M. sorbens is sequenced to better understand the mitogenomic characteristics and phylogeny of this species. The circular mitogenome is 16,120 bp in length, contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), two rRNA genes, and an AT-rich control region. The mitogenome comprises an A + T content of 77.4%. All PCGs start with "ATN" codons except for COI which starts with TCG, and terminate with the common stop codons TNN. A phylogenetic tree, including six Muscidae species, is reconstructed based on the whole mitogenome sequences. The interspecific distances of mitogenomes between the six Muscidae species range from 0.059 to 0.168.

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

Sequencing and analyzing complete mitochondrial DNA of Muscina angustifrons (Insecta, Diptera, Muscidae)

In this study, the complete mitochondrial genome sequenced and analyzed from a fly, Muscina angustifrons which collected from South Korea. The size of mitochondrial genome is 16,316 bp with 40.9% A, 12.3% C, 8.4% G and 38.4% T distribution. Furthermore, phylogenetic relationships of the superfamily Muscoidea evaluated due to mitochondrial protein coding genes. The results showed that the family Muscidae is a paraphyletic group and the closest species to M. angustifrons is M. levida. This is the third complete mitochondrial genome for the genus Muscina and the first genus record from South Korea.

Sequencing and analysis of the complete mitochondrial genome of Aedes albopictus (Diptera: Culicidae) in China

The complete sequence of the mitochondrial genome of the Aedes albopictus (Diptera: Culicidae) is presented using traditional Sanger sequencing. Its mitogenome are 16,660 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding A + T rich region. As in other insects, most mitochondrial genes are encoded on the heavy strand, except for ND5, ND4, ND4L, ND1, two rRNA and eight tRNA genes, which are encoded on the light strand. The overall base composition on heavy strand was as follows - A: 40.1%, G: 8.2%, C: 11.9%, T: 39.8% and the A + T content 79.9%. The results of phylogenetic analyzes showed that the Ae. albopictus has closed relationship with the family Culicidae and order Diptera.