Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Complete Mitochondrial Genome for Lucilia cuprina dorsalis (Diptera: Calliphoridae) from the Northern Territory, Australia

The Australian sheep blowfly, Lucilia cuprina dorsalis, is a major sheep ectoparasite causing subcutaneous myiasis (flystrike), which can lead to reduced livestock productivity and, in severe instances, death of the affected animals. It is also a primary colonizer of carrion, an efficient pollinator, and used in maggot debridement therapy and forensic investigations. In this study, we report the complete mitochondrial (mt) genome of L. c. dorsalis from the Northern Territory (NT), Australia, where sheep are prohibited animals, unlike the rest of Australia. The mt genome is 15,943 bp in length, comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a non-coding control region. The gene order of the current mt genome is consistent with the previously published L. cuprina mt genomes. Nucleotide composition revealed an AT bias, accounting for 77.5% of total mt genome nucleotides. Phylogenetic analyses of 56 species/taxa of dipterans indicated that L. c. dorsalis and L. sericata are the closest among all sibling species of the genus Lucilia, which helps to explain species evolution within the family Luciliinae. This study provides the first complete mt genome sequence for L. c. dorsalis derived from the NT, Australia to facilitate species identification and the examination of the evolutionary history of these blowflies.

The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.

Description of the whole mitochondrial genome of Bhatia longiradiata (Hemiptera, Cicadellidae, Deltocephalinae: Drabescini) and phylogenetic relationship

BACKGROUND

Mitochondrial genomes are extremely conserved in genetic processes and valuable molecular indications for phylogenetic and evolutionary examination, but the mitochondrial genome of Bhatia has not yet been reported.

OBJECTIVE

The target of this writing was to clarify the structural module of the mitochondrial genes of Bhatia longiradiata, verify the monophyletic of Drabescini, and explore the phylogenetic relationship between Drabescini with other leafhoppers.

METHODS

We performed sequencing and explanatory note of the mitochondrion of Bhatia longiradiata. The phylogeny relation was created by ML and Bayesian approaches using three dissimilar datasets (PCG12, PCG12rRNA, and AA), which were constructed to discuss the phylogenetic status of Bhatia longiradiata.

RESULTS

To report the architectural feature of the chondriosome of Bhatia longiradiata is a seal double-stranded annular molecule with 16,122 bp measurement and cover typically 37 genes. Several tandem repetitive units were observed in an AT enrichment area. The analysis showed that the branching relationships among the six trees were generally consistent, and each of the subfamilies was individually clustered into a monophyletic group within Cicadellidae. Bhatia longiradiata and other members of the Drabescini were aggregated into a clade that was situated within the Deltocephalinae.

CONCLUSION

The mitochondrial genome of Bhatia longiradiata covers 37 typical genes and a control region, which covers six tandem repeats. All species of Drabescini procedure a clade within Deltocephalinae. Drabescini and Scaphoideini form a branch and show a sister relationship with strong support. Therefore, we support the relegation of Selenocephalinae to a clan within Deltocephalinae.

Comparative analysis of four complete mitogenomes from hoverfly genus Eristalinus with phylogenetic implications

The genus Eristalinus is widely distributed globally. Four complete mitochondrial genomes (i.e., mitogenomes) of Eristalinus were sequenced and analyzed in this study: Eristalinus viridis (Coquillett, 1898), E. quinquestriatus (Fabricius, 1781), E. tarsalis (Macquart, 1855), and E. sp. Within these four sequenced mitogenomes, most protein-coding genes (ND2, CO1, COX2, COX3, ND3, ND5, ND4, ND4L, ND6, and Cytb) began with a typical ATN (T/C/G/A) start codon and ended with a stop codon TAA or incomplete T, whereas ND1 began with the start codon TTG. ND3 ended with TAG. The secondary tRNA structure was that of a typical cloverleaf, and only the tRNA-Ser1 lacked a DHU arm. Three and five domains appeared in the 12S and 16S rRNA secondary structures, respectively. The phylogenetic relationships among the four Eristalinus species combined with the published mitogenomes of Syrphidae were reconstructed using the maximum likelihood and Bayesian inference methods, which support the monophyly of the subfamily Syrphinae but do not support that of the subfamily Eristalinae. Of note, Eristalini and Syrphini are monophyletic groups. The mitogenomes of E. viridis, E. quinquestriatus, E. sp., and E. tarsalis are useful for determining the phylogenetic relationships and evolution of Syrphidae.

The complete mitochondrial genome of Syritta pipiens (Linnaeus, 1758) (Diptera: Syrphidae) and phylogenetic analysis

The complete mitochondrial genome (mitogenome) of Syritta pipiens (Linnaeus, 1758) was sequenced with 15,745 bp in length including 37 genes and a non-coding region. The overall nucleotide composition showed a strong AT bias. Most protein-coding genes (PCGs) used ATN as the start codon while ATP6 and ND1 used TTG, and stopped by TAA or TAG but ND5 ended with an incomplete T. Phylogenetic trees were reconstructed based on the 24 complete mitochondrial sequences from Syrphidae using the methods of maximum-likelihood (ML) and Bayesian inference (BI), resulted in S. pipiens clustered into the clade of Eristalinae, which conformed to the traditional classification, but the trees did not support the monophyly of Eristalinae. More molecular data is needed for further study.

First mitochondrial genome of the Caucasian squirrel Sciurus anomalus (Rodentia, Sciuridae)

The Caucasian Squirrel, Sciurus anomalus, is the only representative of the Sciuridae family in the Eastern Mediterranean region. In this study, the mitochondrial genome of the Sciurus anomalus species was generated, and we investigate its phylogenetic position within the Sciuridae family. The generated mitogenome sequence is 16,234 bp. It is composed of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes.

The complete mitochondrial genome of Syrphus ribesii (Diptera: Syrphoidea: Syrphidae)

The complete mitochondrial genome of Syrphus ribesii was determined in this study. The double-stranded circular DNA molecule was 16,530 bp in length, containing 37 typical genes: 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and an A + T-rich region. Thirteen PCGs were 11,196 bp in size, encoding 3720 amino acids in total. All the PCGs started with ATN, except the COI used TTG as its initiation codon. Most PCGs terminated with standard codon TAA, while the COI ended with T and the ND5 ended with TA. The lrRNA and srRNA genes were 1341 bp and 793 bp in length, respectively. The A + T-rich region harbored some typical structures characteristic of the dipterans. The phylogenetic tree showed that Syrphus ribesii was closely related to Eupeodes corollae, and the Syrphidae and Pipunculidae constituted a monophyletic group within the Syrphoidea.

The complete mitochondrial genome of Platycheirus albimanus (Diptera: Syrphidae: Syrphinae) and phylogenetic analysis of the Syrphidae

The complete mitochondrial genome of Platycheirus albimanus (Fabricius, 1781) was sequenced. The length of the mitogenome is 16,648 bp and consists of 37 genes including 22 transfer RNA (tRNAs), 13 protein-coding (PCGs) and 2 ribosomal RNA (rRNAs). The 13 PCGs initiate with the start codon ATN, except for COX1 and ATP6 which use TTG. All of the PCGs ended with TAA, apart from ND4 and ND4L terminated by incomplete T––. The ML tree based on complete mitogenomes from 25 species (22 Syrphidae and 3 outgroup taxa) suggests that the tribe Melanostomini is more closely related to the Syrphini. The phylogenetic analysis supports the monophyly of Syrphinae, and the paraphyly of the Eristalinae. This mitogenome information for P. albimanus could facilitate future studies of evolutionarily related insects.

The first complete mitochondrial genome of genus Phytomia (Diptera: Syrphidae)

The complete mitochondrial genome (mitogenome) of Phytomia zonata was sequenced in this study, it is the first complete mitogenome in the genus Phytomia. The wholly sequence is a circular DNA, and with 15,716 bp in length including 37 typical genes. No gene arrangement was observed in this sequence. The common start and stop codons were ATN and TAA, respectively. A phylogenetic tree was generated based on dataset of 19 complete mitogenomes from hoverflies and two Lauxaniidae species which as outgoup, and shows Phytomia is closer to Eristalis, supports the monophyly of Syrphinae.

Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.