The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae

Phylogenomic analysis and molecular identification of true fruit flies

The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.

First report of the complete mitochondrial genome of Carpomya pardalina (Bigot) (Diptera: Tephritidae) and phylogenetic relationships with other Tephritidae

Carpomya pardalina is known for its potential invasiveness, which poses a significant and alarming threat to Cucurbitaceae crops. It is considered a highly perilous pest species that requires immediate attention for quarantine and prevention. Due to the challenges in distinguishing pests of the Tephritidae family based on morphological characteristics, it is imperative to elucidate the mitochondrial genomic information of C. pardalina. In this study, the mitochondrial genome sequence of C. pardalina was determined and analyzed using next-generation sequencing. The results revealed that the mitogenome sequence had a total length of 16,257 bp, representing a typical circular molecule. It consisted of 13 PCGs, two rRNA genes, 22 tRNA genes and a non-coding region. The structure and organization of the mitochondrial genome of C. pardalina were found to be typical and similar to the published homologous sequences of other fruit flies in the Tephritidae family. Phylogenetic analysis confirmed that C. pardalina belongs to the Carpomya genus, which is consistent with traditional morphological taxonomy. Additionally, Carpomya and Rhagoletis were identified as sister groups. This study presents the first report of the complete mitochondrial genome of C. pardalina, which can serve as a valuable resource for future investigations in species diagnosis, evolutionary biology, prevention and control measures.

Next-Generation Sequencing of Four Mitochondrial Genomes of Dolichovespula (Hymenoptera: Vespidae) with a Phylogenetic Analysis and Divergence Time Estimation of Vespidae

The wasp genus Dolichovespula (Hymenoptera: Vespidae: Vespinae) is a eusocial wasp group. Due to the taxonomic and phylogenetic issues with the family Vespidae, more genetic data should be gathered to provide efficient approaches for precise molecular identification. For this work, we used next-generation sequencing (also known as high-throughput sequencing) to sequence the mitochondrial genomes (mtgenomes) of four Dolichovespula species, viz. D. flora, D. lama, D. saxonica, and D. xanthicincta 16,064 bp, 16,011 bp, 15,682 bp, and 15,941 bp in length, respectively. The mitochondrial genes of the four species are rearranged. The A + T content of each mtgenome is more than 80%, with a control region (A + T-rich region), 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. There are 7 to 11 more genes on the majority strands than on the minority strands. Using Bayesian inference and Maximum-Likelihood methodologies as well as data from other species available on GenBank, phylogenetic trees and relationship assessments in the genus Dolichovespula and the family Vespidae were generated. The two fossil-based calibration dates were used to estimate the origin of eusociality and the divergence time of clades in the family Vespidae. The divergence times indicate that the latest common ancestor of the family Vespidae appeared around 106 million years ago (Ma). The subfamily Stenogastrinae diverged from other Vespidae at about 99 Ma, the subfamily Eumeninae at around 95 Ma, and the subfamily Polistinae and Vespinae diverged at approximately 42 Ma. The genus Dolichovespula is thought to have originated around 25 Ma. The origin and distribution pattern of the genus Dolichovespula are briefly discussed.

Complete mitochondrial genome of Dacus vijaysegarani and phylogenetic relationships with congeners and other tephritid fruit flies (Insecta: Diptera)

Background

Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank.

Methods and results

In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific.

Conclusions

Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11033-021-06608-2.

The gene arrangement and phylogeny using mitochondrial genomes in spiders (Arachnida: Araneae)

The complete mitochondrial genome (mitogenome) of Cheiracanthium triviale was sequenced for the first time. The 14,595 bp C. triviale mitogenome contained 37 genes (13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs) and one control region. The mitogenome of Dysdera silvatica which was available at NCBI GenBank was annotated. The mitogenome of C. triviale was compared with 43 previously sequenced spider species to observe the gene arrangements, control region and phylogeny. TreeREx analysis identified 19 mitochondrial gene rearrangements (11 transposition, 6 inversion, 2 inverse transposition) in spiders as compared with the putative ancestral gene order and lead to form new gene boundaries: trnQ-trnA, trnA-trnM for Loxosceles similis; nad3-trnS1, trnE-trnL2, trnL2-trnA, trnN-trnF for Agelena silvatica; trnN-trnE, trnE-trnA, trnR-trnF, nad4L-trnW, trnW-trnP for Carrhotus xanthogramma; trnQ-trnW, trnW-trnG, trnG-trnM for Tetragnatha nitens. Our study revealed that the gene rearrangement in spiders with putative ancestor is accelerated in Araneomorphae as compared to Mygalomorphae. Phylogenetic analysis of spiders using mitochondrial sequence data supports the monophyly of two infraorders, and sister relationship of Cheiracanthiidae with Selenopidae and Salticidae. The systematic position of the Cheiracanthium species always a controversial issue as this taxa was placed in different families by different authors.