Comparative analysis of mitochondrial genomes among the subfamily Sarcophaginae (Diptera: Sarcophagidae) and phylogenetic implications

Contribution to the Diversity of the Genus Sarcophaga (Diptera: Sarcophagidae): Checklist, Species Distribution, and New Records for Greece

The current study presents new records and an updated checklist of the genus Sarcophaga (Diptera: Sarcophagidae) for Greece. The records were compiled from published literature, identification of newly collected material obtained through passive (trapping) and active (hand collecting, net sweeping) sampling conducted between 2018 and 2024, and the examination of material from two museum collections: Entomological Collection of the Goulandris Natural History Museum (1983-1987) and the Melissotheque of the Aegean (2004-2024). After the examination of 927 male specimens from 108 localities and the synthesis of the available literature, a total of 72 species distributed across 18 subgenera were documented. Among these, Sarcophaga ferox (Villeneuve, 1908) and Sarcophaga anaces (Walker, 1849) are newly records for Greece, while Sarcophaga beckiana (Lehrer, 1996) represents the first documented occurrence of the species in Europe. The findings represent the most contemporary contribution to the understanding of the species diversity and distribution of the genus Sarcophaga in Greece.

Study of Mitogenomes Provides Implications for the Phylogenetics and Evolution of the Infraorder Muscomorpha in Diptera

The Muscomorpha is one of the most species-rich brachyceran groups in Diptera, with many species serving as important disease vectors; however, its high-level phylogenetic relationships have long been controversial and unsolved. This study comparatively analyzed the characteristics of mitogenomes of 131 species that represent 18 superfamilies in Muscomorpha, in which mitogenomes of 16 species have been newly sequenced and annotated, demonstrating that their gene composition, order, AT bias, length variation, and codon usage are consistent with documented dipteran mitogenomes. The phylogenetic topologies demonstrated that the robustness of Muscomorpha and major clades within Muscomorpha are monophyletic: Cyclorrhapha, Schizophora, and Calyptratae. A clade of Empidoidea were recovered as the sister group to Cyclorrhapha. Within Cyclorrhapha, Platypezoidea and Syrphoidea were sequentially placed as basal groups of the Cyclorrhapha. The remaining cyclorrhaph superfamilies gathered as two main clades. Ephydroidea were, in most cases, placed as the sister group to Calyptratae. Within Calyptratae, Hippoboscoidea were sister to an assemblage of lineages composed of an Oestroid grade and Muscoidea. The Muscomorpha was proposed to originate in the early Jurassic, and the main clade diversified near the Cretaceous-Paleogene extinction event, estimated using the MCMCtree and six fossil calibration points. The ancestral area of origin and geographic range of Muscomorpha was deduced to be the Palaearctic region with 56.9% probability using the RASP software based on a dated tree.

First Report and Phylogenetic Analysis of Mitochondrial Genomes of Chrysomya villeneuvi and Sarcophaga genuforceps

The mitochondrial genome, highly conserved across species, is crucial for species identification, phylogenetic analysis, and evolutionary research. Chrysomya villeneuvi and Sarcophaga genuforceps, two species with significant forensic value, have been understudied in terms of genetic data. In this study, the complete mitochondrial genomes of C. villeneuvi (15,623 bp) and S. genuforceps (15,729 bp) were sequenced and analyzed. All thirteen protein-coding genes (PCGs) exhibited Ka/Ks ratios below one, indicating purifying selection and supporting their utility as barcoding markers. Phylogenetic analysis and genetic distance calculations based on PCGs showed that C. villeneuvi is closely related to Chrysomya rufifacies and Chrysomya albiceps, and S. genuforceps aligns more closely with Sarcophaga kentejana and Sarcophaga schuetzei. This research is the first to provide mitochondrial genome data for C. villeneuvi and S. genuforceps, expanding the genetic resources available for Calliphoridae and Sarcophagidae and offering a foundation for further forensic and evolutionary studies.

Research Status of Sarcosaprophagous Beetles as Forensic Indicators

In forensic entomology, research focused on sarcosaprophagous flies, but the sarcosaprophagous beetles, as important "forensic indicator species" of late-stage PMI in cadaver decomposition, received less attention. To increase attention on, and use and understanding of, sarcosaprophagous beetles in forensic entomology, this paper presents a bibliometric analysis of the available relevant literature. The occurrence frequency of beetle families and species from succession studies, actual cases, and experiments were calculated and illustrated using graphs. As a result, a total of 14 families and 1077 species associated with carcasses were collected, with Staphylinidae being the most frequently recorded among the families, and Necrobia rufipes (Fabricius, 1781) (Coleoptera: Cleridae) being the most frequently recorded species. In addition, a brief introduction of the cadaver-related beetles of each family is given, and research on the species identification of the immature stages, age estimation of the immature stages, and estimation of the arrival time of sarcosaprophagous beetles are discussed and prospected. This work will aid in the increased use of sarcosaprophagous beetles in forensic science practice in the future.

Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies

Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.

The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis

BACKGROUND

Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus.

RESULTS

In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis.

CONCLUSIONS

Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.

The complete mitochondrial genome of Sarcophaga angarosinica (Diptera: Sarcophagidae)

Sarcophaga (Liosarcophaga) angarosinica (Rohdendorf, 1937) (Diptera: Sarcophagidae) is a species of both medical and ecological significance. In this study, the complete mitochondrial genome (mitogenome) of S. angarosinica was sequenced and characterized. The mitogenome has a total length of 15,215 bp, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an adenine and thymine-rich region. This mitogenome comprises 39.5% adenine, 9.4% guanine, 14.4% cytosine, and 36.8% thymine. Phylogenetic analysis revealed that S. angarosinica is closely related to Sarcophaga similis. This study enriches the genetic data on S. angarosinica and will contribute to establishing the phylogenetic relationships among flesh flies.

Geographical Distribution and Multimethod Species Identification of Forensically Important Necrophagous Flies on Hainan Island

Forensic entomology offers unique advantages for the minimum postmortem interval (PMImin) estimation of decomposed corpses in forensic investigations. Accurate species identification and up-to-date locality information are essential. Hainan Island has a tropical rainforest climate and a vast territory. In this study, the community structure of necrophagous flies on Hainan Island was investigated in detail according to geographical environment. The results showed that the dominant species included C. megacephala, S. peregrina, C. rufifacies, S. misera, H. ligurriens, S. sericea, S. cinerea, S. dux, C. pinguis, and M. domestica. Furthermore, C. rufifacies and C. villeneuvi were found only in the high-altitude areas of Wuzhi Mountain, while S. cinerea was distributed only in coastal areas; the latter is a representative species of Hainan Island and has not been reported before. Furthermore, a GenBank database of forensically important flies was established, whilst a high-resolution melt (HRM) curve analysis was applied to identify the common species of Hainan Island for the first time. This study enriches the database of forensically important flies in tropical rainforest regions.

The complete mitochondrial genome of Neolissochilus soroides (Duncker, 1904) (Cypriniformes: Cyprinidae)

In this paper, we first report the complete mitochondrial genome of Neolissochilus soroides. The main purpose of this study was to determine the mitochondrial genome and phylogenetic status of N. soroides. The length mitogenome was 16584 bp, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and 3 non-coding control regions. The genome showed a slight A + T bias (A + T = 56.47%). 12 genes (ND1, COX2, ATP6, ND4L, ND5, ND6, ND2, ATP8, ND3, ND4, Cytb, COX3) start with ATG codon, besides one gene (COX1) start with GTG codon. Six genes (ND1, COX1, ATP6, ND4L, ND5, ND6) end with a TAA codon, 3 genes (ND2, ATP8, ND3) end with a TAG codon, and four genes (COX2, ND4, Cytb, COX3) end with the TA or T codon. The phylogenetic analysis showed that N. soroides was closely related to N. hendersoni. The mitogenome could have important implications for phylogeny, population genetics, and conservation of the N. soroides.

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.

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

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.

Development of Forensically Important Sarcophaga peregrina (Diptera: Sarcophagidae) and Intra-Puparial Age Estimation Utilizing Multiple Methods at Constant and Fluctuating Temperatures

Sarcophaga peregrina (Robineau-Desvoidy, 1830) has the potential to estimate the minimum postmortem interval (PMI_min). Development data and intra-puparial age estimation are significant for PMI_min estimation. Previous research has focused on constant temperatures, although fluctuating temperatures are a more real scenario at a crime scene. The current study examined the growth patterns of S. peregrina under constant (25.75 °C) and fluctuating temperatures (18-36 °C; 22-30 °C). Furthermore, differentially expressed genes, attenuated total reflectance Fourier-transform infrared spectroscopy, and cuticular hydrocarbons of S. peregrina during the intra-puparial period were used to estimate age. The results indicated that S. peregrina at fluctuating temperatures took longer to develop and had a lower pupariation rate, eclosion rate, and pupal weight than the group at constant temperatures did. Moreover, we found that six DEG expression profiles and ATR-FTIR technology, CHCs detection methods, and chemometrics can potentially estimate the intra-puparial age of S. peregrina at both constant and fluctuating temperatures. The findings of the study support the use of S. peregrina for PMI_min estimation and encourage the use of entomological evidence in forensic practice.

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 Fannia canicularis (Diptera: Fanniidae)

Fannia canicularis (Linnaeus, 1761) is a species from the family Fanniidae. In this study, we sequenced and analyzed the complete mitochondrial genome of F. canicularis for the first time. The circular mitogenome is 15,826 bp in length, and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region. The family Fanniidae formed a monophyletic clade in the phylogenetic tree based on 13 concatenated PCGs, sister to three other families in Diptera.

Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny

Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.

Phylogenetic Analysis of Mitochondrial Genome of Tabanidae (Diptera: Tabanidae) Reveals the Present Status of Tabanidae Classification

Simple Summary

Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. Therefore, six newly completed mitochondrial genomes of four genera of Tabanidae (Haematopota turkestanica, Chrysops vanderwulpi, Chrysops dissectus, Tabanus chrysurus, Tabanus pleskei, and Hybomitra sp. species) were sequenced and analyzed. The results show that the six newly mitochondrial genomes have quite similar structures and features. Phylogeny was inferred by analyzing the 13 amino acid sequences coded by mitochondrial genes of 22 mitogenomes (all available complete mitochondrial genomes of tabanidae). Bayesian inference, maximum likelihood trees, and maximum parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all groups, ratifies the current taxonomic classification, and provides useful genetic markers for studying the molecular ecology, systematics, and population genetics of Tabanidae.

Abstract

Tabanidae suck the blood of humans and animals, are important biological vectors for the transmission of diseases, and are of considerable economic and medical significance. However, current knowledge about the mitochondrial genome of this family is limited. More complete mitochondrial genomes of Tabanidae are essential for the identification and phylogeny. Therefore, this study sequenced and analyzed six complete mitochondrial (mt) genome sequences of four genera of Tabanidae for the first time. The complete mt genomes of the six new sequences are circular molecules ranging from 15,851 to 16,107 base pairs (bp) in size, with AT content ranging from 75.64 to 77.91%. The six complete mitochondrial genomes all consist of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (RRNA), 22 transfer RNA genes (tRNAs), and a control region, making a total of 37 functional subunits. ATT/ATG was the most common start codon, and the stop codon was TAA of all PCGS. All tRNA except tRNA Ser1 had a typical clover structure. Phylogeny was inferred by analyzing the 13 concatenated amino acid sequences of the 22 mt genomes. Bayesian inference, maximum-likelihood trees, and maximum-parsimony inference analyses all showed consistent results. This study supports the concept of monophyly of all genus, ratifies the current taxonomic classification, and provides effective genetic markers for molecular classification, systematics, and genetic studies of Tabanidae.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae

Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.

Comparative Analysis of Mitochondrial Genomes among Twelve Sibling Species of the Genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae) and Phylogenetic Analysis

Simple Summary

Atkinsoniella is a large genus of 98 species across the world and 88 species recorded in China within the globally distributed subfamily Cicadellinae, which is phytophagous, and some of which have been reported as important agricultural pests. Some Atkinsoniella species are very similar in morphological characteristics, making accurate identification at species level confusing. To provide further evidence toward understanding the relationships within the genus Atkinsoniella and subfamily Cicadellinae, mitogenomes of 12 Atkinsoniella sibling species were obtained and annotated. Their characteristics were comparatively analyzed. In addition, the comprehensive phylogenetic relationship within the subfamily Cicadellinae was determined based on three mitochondrial datasets using both the maximum-likelihood (ML) and Bayesian inference (BI) methods. The results suggested that the genus Atkinsoniella was recovered as a monophyletic group. The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses, indicating that mitogenomics is an effective method for identifying closely related species and understanding their phylogenetic and evolutionary relationships.

Abstract

The herbivorous leafhopper genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae), a large genus of subfamily Cicadellinae, consists of 98 valid species worldwide and 88 species recorded in China. Some species of the genus are very similar in morphological characteristics, so they are difficult to identify accurately. In this study, 12 mitochondrial genomes of Atkinsoniella species with similar morphological characteristics were first obtained through high-throughput sequencing, which featured a typical circular molecule of 15,034–15,988 bp in length. The arrangement and orientation of 37 genes were identical to those of typical Cicadellidae mitogenomes. The phylogenetic relationship within the subfamily Cicadellinae was reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on three concatenated datasets. The topological structures of the six obtained phylogenetic trees were highly consistent. The results suggested that Atkinsoniella was recovered as a monophyletic group and emerged as a sister group with the monophyletic clade of Bothrogonia, Paracrocampsa (part), and Draeculacephala (part). The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses. In addition, the key to the 12 Atkinsoniella species was provided to identify species according to morphological characteristics. This study further promotes research on the classification, genetics, evolution, and phylogeny of the genus Atkinsoniella and subfamily Cicadellinae.

Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications

The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.

Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and molecular evolution. In this study, the complete mitogenomes of two hermit crabs, Dardanus arrosor and Dardanus aspersus, were sequenced for the first time and compared with other published mitogenomes of Paguroidea. Each of the two mitogenomes contains an entire set of 37 genes and a putative control region, but they display different gene arrangements. The different arrangements of the two mitogenomes might be the result of transposition, reversal, and tandem duplication/random loss events from the ancestral pancrustacean pattern. Genome sequence similarity analysis reveals the gene rearrangement in 15 Paguroidea mitogenomes. After synteny analysis between the 15 Paguroidea mitogenomes, an obvious rearranged region is found in D. aspersus mitogenome. Across the 13 protein-coding genes (PCGs) tested, COI has the least and ND6 has the largest genetic distances among the 15 hermit crabs, indicating varied evolution rates of PCGs. In addition, the dN/dS ratio analysis shows that all PCGs are evolving under purifying selection. The phylogenetic analyses based on both gene order and sequence data present the monophyly of three families (Paguridae, Coenobitidae, and Pylochelidae) and the paraphyly of the family Diogenidae. Meanwhile, the phylogenetic tree based on the nucleotide sequences of 13 PCGs shows that two Dardanus species formed a sister group with five Coenobitidae species. These findings help to better understand the gene rearrangement and phylogeny of Paguroidea, as well as provide new insights into the usefulness of mitochondrial gene order as a phylogenetic marker.

The complete mitochondrial genome of Sarcophaga tsinanensis (Diptera: Sarcophagidae)

Sarcophaga tsinanensis (Fan, 1964) (Diptera: Sarcophagidae), a species from subgenus Heteronychia. In this study, we report the complete mitochondrial genome (mitogenome) of S. tsinanensis. The length of this mitogenome was 14,972 bp in total, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. The arrangement of genes was the same as that of ancestral metazoan. Sarcophaga tsinanensis has a high nucleotide bias in A/T accounting for 76.80% of total nucleotides (A 39.9%, G 9.2%, C 13.9%, and T 36.9%). The result of phylogenetic analysis revealed that S. tsinanensis cluster together with species from the same subgenus Heteronychia, showing a clear monophyletic relationship. Sarcophaga tsinanensis is closely related to its sister species Sarcophaga depressifrons, Sarcophaga plotnikovi, and Sarcophaga shnitnikovi. This study provides the mitochondrial data of S. tsinanensis for further research on evolutionary relationships and species identification of flesh flies.

Characterization of the complete mitochondrial genomes of six horseflies (Diptera: Tabanidae)

The family Tabanidae (Insecta: Diptera) is one of the economically most important group of haematophagous insects, causing millions of livestock deaths per year. However, current knowledge on the mitochondrial genomes (mitogenomes) from this family is limited. Additional tabanid mitogenomes characterization is of utmost importance for their identification, epidemiologic and phylogenetic studies. We sequenced the mt genomes of six horseflies with an Illumina platform and their phylogenetic relationship was conducted with other infraorder Tabanomorpha members with available mt genome datasets. All six newly sequenced mitogenomes were typical 37-gene circular structures retaining the gene order of Tabanomorpha. The trnQ, trnM and trnA were highly conserved among the six mitogenomes (identity = 100%). The TΨC arm and variable loop regions were relatively more variable compared to the amino acid receptor arm, anticodon arm and DHU arm of the tRNAs. Among 13 protein-coding genes (PCGs) of tabanids mitogenomes, the highest nucleotide diversity was detected in atp8, cox1, cox3, nad6 and cytb (0.1 for each). In addition, atp8 genes exhibited the highest evolutionary rate (ω = 0.24) among 13 PCGs. The interspecies K2P genetic distances among some Tabanus spp. across the mitogenome was greater (0.08) than intergeneric genetic distance between T. amaenus and Atylotus miser (0.07). Phylogenetic analyses revealed non-monophyletic relationships among horseflies of the genus Tabanus. The present study showed mt gene order is highly conserved within Tabanus species. Our mito-phylogenomic analysis supports the paraphyly of the genus Tabanus. The new data provide novel genetic markers for studies of population genetics and systematics of horseflies.

The complete mitochondrial genome of Sarcophaga gracilior (Diptera: Sarcophagidae)

Sarcophaga gracilior Chen, 1975 (Diptera: Sarcophagidae) plays a significant role in epidemiology and medicine. In this study, we first report the complete mitochondrial genome (mitogenome) of S. gracilior. This mitogenome was 15,534 bp in length (GenBank No. MW531675), comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The arrangement of genes was identical to that of ancestral metazoan. Nucleotide composition revealed a strong A + T bias, accounting for 76.7% (A 39.6%, G 9.3%, C 14.0%, T 37.1%). The phylogenetic relationships indicated that the species of S. gracilior emerged as sister to Sarcophaga melanura. This study provides important mitochondrial data for further studying evolutionary relationships and species identification of flesh flies.

The complete mitochondrial genome of Fannia scalaris (Diptera: Muscidae)

Fannia scalaris (Fabricius, 1794) is closely related to human life in ecological habits, which can lead to health concerns since they feed on various contamination sources. In this study, we first present the mitochondrial genome (mitogenome) of F. scalaris (GenBank No. MT017706). The length of this mitogenome was composed of 15,040 base pairs, including 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA, and an AT-rich region. It consisted of A 39.3%, G 9.1%, C 13.0%, and T 38.6%. The arrangement of the genes was consistent with that of the ancestral metazoan. Furthermore, phylogenetic relationship indicated that F. scalaris was obviously separated from the muscid flies. This study provides useful genetic data in order to further understand the evolutionary relationship of the Muscidae.

The complete mitochondrial genome of Sarcophila mongolica (Diptera: Sarcophagidae)

Sarcophila mongolica Chao & Zhang, 1988 (Diptera: Sarcophagidae) is considered to be of ecological and medical significance. In this study, we report the mitochondrial genome (mitogenome) of S. mongolica. This mitogenome was composed of 15,936 bp in length (GenBank accession no. MT845211), comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The arrangement of genes was identical to that of ancestral metazoan. Nucleotide composition revealed a strong A + T bias, accounting for 75.40% (A 38.2%, G 9.7%, C 14.9%, and T 37.2%). Phylogenetic analysis indicated that S. mongolica was obviously separated from the other flesh flies. This mitogenome provides important genetic data for further understanding of the evolutionary relationship within Sarcophagid flies.

Comparative analysis of the mitochondrial genomes of flesh flies and their evolutionary implication

Flesh flies (Diptera: Sarcophagidae) include a large and widely distributed rapid radiation within the Calyptratae. They are vital for the ecosystem, as well as economic, forensic, and evolutionary studies, because of their extremely diverse habits as larvae. Phylogenetic studies of Sarcophagidae have been reaching convergence, which leads the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome. Complete mitochondrial genomes of eight species were sequenced, and comparative mitochondrial genomic analysis between subfamilies were conducted. Mitochondrial genomes of these flesh flies are conserved in gene content with gene arrangement, same as the inferred ancestral insect, and the nucleotide composition is highly biased towards A + T like other flesh flies. The evolutionary rates of Sarcophagidae vary considerably across subfamilies, with that of Miltogramminae higher than the other two subfamilies. Phylogenetic analysis strongly supports monophyly of Sarcophagidae and each subfamily, with subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). The main topological inconsistency of all reconstructions is the relationship within Miltogramminae and Sarcophaga, which might be caused by their rapid evolution. Our study indicates that the mitochondrial genomes of flesh flies are highly conserved, and they are practically useful for phylogenetic inference of calyptrates.

The complete mitochondrial genome of Muscina pascuorum (Diptera: Muscidae)

Muscina pascuorum (Diptera: Muscidae) represents an important hygiene pest. The complete mitochondrial genome (mitogenome) of M. pascuorum was first sequenced and annotated in this study. The full length of mitogenome was 14, 940 bp, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA), 22 transfer RNA (tRNA), and one AT-rich region. The nucleotide content of these flies was 40.0% A, 13.2% C, 9.1% G, and 37.6% T. This study illustrates that the arrangement of the genes was identical to classical metazoans. Besides, the phylogenetic analyses indicated that the branch of M. pascuorum was clustered separately from the common three Muscina spp in the tree. This genome provides an essential reference for understanding the phylogenetic relationships of Muscidae.