The complete mitochondrial genome of Aphaenogaster famelica (Smith, 1874) (Hymenoptera: Formicidae)

De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes

Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.

Complete Nucleotide Sequence of the Mitogenome of Tapinoma ibericum (Hymenoptera: Formicidae: Dolichoderinae), Gene Organization and Phylogenetics Implications for the Dolichoderinae Subfamily

The ant Tapinoma ibericum Santschi, 1925 is native to the Iberian Peninsula. This species, as well as other species from the Tapinoma nigerrimum complex, could form supercolonies that make these species potentially invasive and could give rise to pests. Recently a mature colony from this species has been found in the Isle of Wight (United Kingdom). Mitogenomes have been used to study the taxonomy, biogeography and genetics of species, improving the development of strategies against pest invasion. However, the number of available mitogenomes from the subfamily Dolichoderinae is still scarce and only two of these mitogenomes belong to Tapinoma species. Herein, the complete mitogenome of T. ibericum is presented in order to increase the molecular information of the genus. The T. ibericum mitogenome, retrieved by Next-Generation Sequencing data, is 15,715 bp in length. It contains the typical set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs and the A + T-rich control region. Comparisons of the T. ibericum mitogenome with other dolichoderine mitogenomes revealed the existence of four gene rearrangements in relation with the ancestral insect mitogenome. One of these rearrangements, involving the tRNA-Ile, tRNA-Gln and tRNA-Met genes, was found in most of the analyzed ant mitogenomes. Probably this rearrangement was an ancestral or plesiomorphic character in Formicidae. Interestingly, another rearrangement that affects to tRNA-Trp, tRNA-Cys and tRNA-Tyr genes was found only in Tapinoma species. This change could be a synapomorphic character for the genus Tapinoma, and could be used as a phylogenetic marker. Additionally, a phylogenetic analysis was performed using the protein-coding gene sequences from available Dolichoderinae mitogenomes, as well as mitogenomes from representative species from other Formicidae subfamilies. Results support the monophyletic nature of the genus Tapinoma placing it within the same clade as the rest of Dolichoderinae species.

The complete mitochondrial genome of Aphaenogaster japonica (Forel, 1911) (Hymenoptera: Formicidae)

Aphaenogaster japonica (Forel, 1911) is an omnivorous ant that is widely distributed in eastern Asia. The mitochondrial genome of A. japonica reported here was 18,607 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The base composition was AT biased (the GC ratio is 18.9%). With A. japonica added, we obtain weak evidence that the sister group of the Stenammini group, including Aphaenogaster, is the Myrmicini group. Therefore, the Stenammini and Myrmicini groups may be not a robust monophyletic group, unlike the previous results based on the complete mitochondrial genome.

The complete mitochondrial genome of Pheidole nodus (Smith, 1874) (Hymenoptera: Formicidae)

Pheidole nodus (Smith, 1874) belongs to a famously hyperdiverse and ecologically dominant ant genus. The mitochondrial genome of P. nodus is 15,579 bp in length, and the overall base composition is 78.6% AT. It includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. Phylogenetic trees show that P. nodus is more closely related to Wasmannia than to Atta. These sequence data will play an important role in the investigation of the phylogenetic relationships and taxonomy of the group Attini.

The complete mitochondrial genome of Tetramorium tsushimae (Emery, 1925) (Hymenoptera: Formicidae)

Tetramorium tsushimae (Emery, 1925) is an omnivorous ant species native to East Asia and has been introduced to North America. The mitochondrial genome of T. tsushimae is 19,207 bp in length with an A + T content of 81.3% and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. This sequence data would play an important role in the investigation of mitochondrial evolution of the subfamily Myrmicinae.

A New Mitochondrial Genome of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) and Mitogenome-Wide Investigation on Polymorphisms

Simple Summary

We completed one mitogenome of white-backed planthopper (WBPH), Sogatella furcifera (Horváth), with finding heteroplasmy phenomenon confirmed by PCR reaction and Sanger sequencing method. This heteroplasmy was not observed in WBPHs (n = 24) collected from the fields, suggesting that it may be uncommon in fields. We also analyzed single nucleotide polymorphisms, insertion and deletions, and simple sequence repeats among three currently available WBPH mitogenomes of Korea and China, suggesting that identified intraspecific variations could be potential candidates for developing markers to distinguish geographical populations of WBPH including Korean and Chinese. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade.

Abstract

White-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the major sap-sucking rice pests in East Asia. We have determined a new complete mitochondrial genome of WBPH collected in the Korean peninsula using NGS technology. Its length and GC percentages are 16,613 bp and 23.8%, respectively. We observed one polymorphic site, a non-synonymous change, in the COX3 gene with confirmation heteroplasmy phenomenon within individuals of WBPH by PCR amplification and Sanger sequencing, the first report in this species. In addition, this heteroplasmy was not observed in wild WBPH populations, suggesting that it may be uncommon in fields. We analyzed single nucleotide polymorphisms, insertion, and deletions, and simple sequence repeats among the three WBPH mitogenomes from Korea and China and found diverse intraspecific variations, which could be potential candidates for developing markers to distinguish geographical populations. Phylogenetic analysis of 32 mitogenomes of Delphacidae including the three WBPH mitogenomes suggested that Delphacinae seems to be monophyletic and Sogatella species including WBPH are clearly formed as one clade. In the future, it is expected that complete mitogenomes of individuals of geographically dispersed WBPH populations will be used for further population genetic studies to understand the migration pathway of WBPH.

The complete mitochondrial genome of a parthenogenetic ant Monomorium triviale (Hymenoptera: Formicidae)

Monomorium is one of the most species-rich yet taxonomically problematic ant genus. An East Asian species, M. triviale Wheeler, W.M., 1906, is reproduced by obligate thelytokous parthenogenesis and performs strict reproductive division of labor. We sequenced the M. triviale mitogenome using next-generation sequencing methods. The circular mitogenome of M. triviale was 16,290 bp in length, consisting of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single non-coding region of 568 bp. The base composition was AT-biased (82%). Gene order rearrangements were detected and likely to be unique to the genus Monomorium. We announce the M. triviale mitogenome as additional genomic resources for elucidating phylogenetic and taxonomic problems of Monomorium and comparative genomics of parthenogenetic ant species.

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.

Complete mitochondrial genome of the H3 haplotype Argentine ant Linepithema humile (Mayr, 1868) (Formicidae; Hymenoptera)

The argentine ant, Linepithema humile (Mayr, 1867), is an invasive ant species that has spread across the world. We have determined the mitochondrial genome of L. humile collected in South Korea, which is 15,934 bp containing 10 SNPs and 5 INDELs compared to the previous mitogenome. Most SNPs were found in cox3, followed by cytb. From SNPs our mitogenome was identified as a H3 haplotype, which was previously recorded in Japan and the U.S. while the previous mitogenome was H1 haplotype. Phylogenetic analysis was congruent to previous study within the tribe Leptomyrmecini but not between other tribes of subfamily Dolichoderinae.

Complete mitochondrial genome of the jet ant Lasius spathepus Wheeler, W.M., 1910 (Formicidae; Hymenoptera)

The genus Lasius is a conspicuous and popular genus of ants found in the Holarctic regions. We have completed the mitochondrial genome of Lasius spathepus as the first mitochondrial genome of Lasius. The mitochondrial genome is 18,951 bp long, which is the sixth longest ant mitochondrial genome known to science. It contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region in a gene order shared with other species of subfamily Formicinae. The control region is 2,147 bp long, longest of all ants. Phylogenetic analysis shows L. spathepus groups with Nylanderia flavipes of the same tribe Lasiini.