Hemiptera Mitochondrial Control Region: New Sights into the Structural Organization, Phylogenetic Utility, and Roles of Tandem Repetitions of the Noncoding Segment

Structures and genetic information of control region in mitogenomes of Odonata

Mitogenome data of Odonata is accumulating and widely used in phylogenetic analysis. However, noncoding regions, especially control region, were usually omitted from the phylogenetic reconstruction. In an effort to uncover the phylogenetic insights offered by the control region, we have amassed 65 Odonata mitogenomes and conducted an examination of their control regions. Our analysis discovered that species belonging to Anisoptera and Anisozygoptera exhibited a stem-loop structure, which was formed by a conserved polyC-polyG stretch located near the rrns gene (encoding 12S rRNA). Conversely, the polyC-polyG region was not a conserved fragment in Zygoptera. The length and number of repetitions within the control region were identified as the primary determinants of its overall length. Further, sibling species within Odonata, particularly those in the genus Euphaea, displayed similar patterns of repetition in their control region. Collectively, our research delineates the structural variations within the control region of Odonata and suggests the potential utility of this region in elucidating phylogenetic relationships among closely related species.

Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae)

Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.

Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.

Comparative and phylogenetic analyses of mitochondrial genomes in Elateridae (Coleoptera: Elateroidea)

The click-beetles (Elateridae) are a species-rich beetle family that is easily recognizable. They are distributed in all zoogeographical regions with over 11,000 species. Comparative studies of the structural characteristics of mitochondrial genomes (mitogenomes), as well as phylogenetic relationships of click-beetles, can improve our understanding of mitogenomic evolution. In this study, we determined four mitogenomes from Elateridae by next-generation sequencing. The four mitogenomes were 16,005 to 16,930 bp in length with 37 typical genes and a control region (A + T-rich region). Combined with previously reported elaterid mitogenomes, all PCGs initiate with either the standard start codon of ATN or TTG. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively. Among the control regions of the four mitogenomes, several different patterns and numbers of tandem repeats were identified, which was the primary cause of the length variation in control regions. Phylogenetic analyses were conducted based on 13 protein-coding genes and two ribosomal RNA genes from 33 species of Elateridae and two outgroups. The Bayesian inference and maximum likelihood trees had an identical topological structure. The monophyly of Cardiophorinae, Agrypninae and Elaterinae was recovered with high support in all topologies, and the Tetralobinae was placed as the earliest branch in the Elateridae. Expanding the availability of mitogenomic and genomic data from a broader range of click-beetles could provide more clarity on the disputed relationships among subfamilies within Elateridae.

Features and evolution of control regions in leafroller moths (Lepidoptera: Tortricidae) inferred from mitochondrial genomes and phylogeny

The control region (CR) of the mitochondrial genome (mitogenome) represents a major noncoding fragment with several special structural features that are thought to be responsible for the initiation of mitogenome transcription and replication. However, few studies have revealed the evolutionary patterns of CR in the phylogenetic context. Here, we explain the characteristics and evolution of CR in Tortricidae, inferred from a mitogenome-based phylogeny. The first complete mitogenomes of the genera Meiligma and Matsumuraeses were sequenced. Both mitogenomes are double-stranded circular DNA molecules with lengths of 15,675 bp and 15,330 bp, respectively. Phylogenetic analyses derived from 13 protein-coding genes and two ribosomal RNAs showed that most tribes, including subfamilies Olethreutinae and Tortricinae, were recovered as monophyletic clades, similar to previous studies based on morphological or nuclear data. Moreover, comprehensive comparative analyses of the structural organization and role of tandem replications on the length variation and high AT content of CR sequences were conducted. The results reveal a significant positive correlation between the total length and AT content of tandem repeats and whole CR sequences in Tortricidae. The structural organization in CR sequences is diverse, even between closely related tribes, which demonstrates the plasticity of the mitochondrial DNA molecule in Tortricidae.

Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites

Mites from the Acaroidea (Sarcoptiformes: Astigmatina) are important pests of various stored products, posing potential threats to preserved foods. In addition, mites can cause allergic diseases. Complete mitochondrial genomes (mitogenomes) are valuable resources for different research fields, including comparative genomics, molecular evolutionary analysis, and phylogenetic inference. We sequenced and annotated the complete mitogenomes of Thyreophagus entomophagus and Acarus siro. A comparative analysis was made between mitogenomic sequences from 10 species representing nine genera within Acaroidea. The mitogenomes of T. entomophagus and A. siro contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region. In Acaroidea species, mitogenomes have highly conserved gene size and order, and codon usage. Among Acaroidea mites, most PCGs were found to be under purifying selection, implying that most PCGs might have evolved slowly. Our findings showed that nad4 evolved most rapidly, whereas cox1 and cox3 evolved most slowly. The evolutionary rates of Acaroidea vary considerably across families. In addition, selection analyses were also performed in 23 astigmatid mite species, and the evolutionary rate of the same genes in different superfamilies exhibited large differences. Phylogenetic results are mostly consistent with those identified by previous phylogenetic studies on astigmatid mites. The monophyly of Acaroidea was rejected, and the Suidasiidae and Lardoglyphidae appeared to deviate from the Acaroidea branch. Our research proposed a review of the current Acaroidea classification system.

First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae (Coleoptera: Tenebrionoidea)

Despite worldwide distribution and rich diversity, the knowledge of mitochondrial genome (mtgenome) characteristics within the family Tenebrionidae (Coleoptera) is still very limited, and phylogenetics remain unresolved for the family. In this study, the mtgenomes for 12 species are newly sequenced and annotated. Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae. Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome, and AT bias, length variation, and codon usage are consistent with other reported beetle mtgenomes. Some intergenic overlap and gap sequences may contain phylogenetically informative information, whereas neither the conserved nor repeat sequences in the control region do. The subfamilies Lagriinae, Pimeliinae, Stenochiinae, and Alleculinae are found to be monophyletic, and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study. Furthermore, Lagriinae is sister to the rest of the subfamilies. At the tribal level, the tribes Lagriini in the subfamily Lagrrinae; Strongyliini in Stenochiinae; Cteniopodini in Alleculinae; and Triboliini, Opatrini, and Amarygmini in Tenebrioninae are monophyletic; while Diaperini in Diaperinae, and Tenebrionini in Tenebrioninae are polyphyletic.

Characterization of the mitochondrial genomes of Bradysia hygida, Phytosciara flavipes and Trichosia splendens (Diptera: Sciaridae) and novel insights on the control region of sciarid mitogenomes

Sciarids, also called "fungus gnats" are small, almost entirely dark-coloured insects. Sciarid larvae feed on different substrates and can infest agricultural crops and mushroom nurseries, causing economic losses. Of the 2174 Diptera mitogenome sequences currently available in GenBank, only eight are from the Sciaridae family, none of which are complete circular molecules. Here we describe the mitogenome sequences of three sciarid species: Phytosciara flavipes, Trichosia splendens and Bradysia hygida and provide novel insights on the control region of sciarid mitogenomes. The assembled mitogenomes range from 16,062 bp in P. flavipes to 17,095 bp in B. hygida. All 13 protein coding genes, 22 tRNAs and 2 rRNAs characteristic of insect mitogenomes were identified, but the sequence of the control region could not be determined. Experimental results suggest that the B. hygida control region is about 21 kb long resulting in a 37 kb long mitogenome which constitutes the largest insect mitochondrial genome described so far. Phylogenetic analysis using all Bibionomorpha mitogenome sequences available in GenBank strongly supports the Sciaridae monophyly and led to the identification of species and subfamily specific gene rearrangements. Our study extends the knowledge of this large and diverse insect family that includes agricultural pest species.

Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes

BACKGROUND

Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results.

METHODS AND RESULTS

The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum.

CONCLUSIONS

The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.

Comparative mitochondrial genomes of the Rhus gall aphid Kaburagia rhusicola subspecies with variable gall shapes

Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae) stimulate the formation of galls on their primary host plants (sumacs: Rhus spp., Anacardiaceae). The shapes of galls are often used as an extended phenotype to identify the aphid species and subspecies. We collected four Rhus galls with conspicuously different shapes formed by Kaburagia rhusicola aphids, whose sequences of the complete mitochondrial genomes (mitogenomes) were obtained by high-throughput sequencing. Each mitogenome was assembled into a circular molecule containing 13 protein-coding genes, two rRNAs, 22 tRNAs and one control region. All the protein-coding genes had a typical ATN initiation codon and TAA termination codon except for cox1 and nad4, which had a single T as stop codon. All the tRNAs could be folded as a typical clover-leaf secondary structure, except for trnS1 lacking a dihydrouridine (DHU) arm. The relative synonymous codon usage and ratio of nonsynonymous to synonymous substitution rates showed that the four K. rhusicola samples were highly similar to the subspecies K. r. ovogallis. The phylogenetic analyses grouped these samples with K. r. ovogallis in a clade sister to K. r. rhusicola. All these molecular analyses demonstrated that our current samples represented one subspecies of Kaburagia rhusicola, i.e., K. r. ovogallis, and the gall shape was variable even at the subspecies level in Kaburagia gall aphids.

Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea

The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS₂ junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.

Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies

Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America.

Comparative mitogenomes of six species in the subfamily Iassinae (Hemiptera: Cicadellidae) and phylogenetic analysis

For elucidating phylogenetic relationships among members of the family Cicadellidae, mitogenomes of six members of the subfamily Iassinae, including Batracomorphus lateprocessus, Iassus dorsalis, Krisna concava, Krisna rufimarginata, Gessius rufidorsus, and Trocnadella arisana, were sequenced. The mitogenomes are 14,724-15,356-bp long. Moreover, typical 37 genes in mitogenomes were identified; arrangement of these genes in the studied species was consistent with that in the inferred ancestral insects, except for tRNA genes, with a simple switch between the positions of trnI and trnQ in Trocnadella arisana. Most protein-coding genes in the Iassinae mitogenomes showed typical ATN start codons (ATA/ATT/ATC/ATG) and TAR (TAA/TAG) or an incomplete stop codon T--; ATP8 of all sequenced species showed the start codon TTG. The secondary structures of 16S rRNA and 12S rRNA were predicted. 16S rRNA comprised 6 domains with 43 helices, and 12S rRNA comprised 3 domains with 25 helices. All subfamilies, except Cicadellinae and Evacanthinae, were recovered as monophyletic. As reported previously, treehoppers originated from paraphyletic Cicadellidae. Iassinae and Coelidiinae, Megophthalminae and treehoppers, and Cicadellinae and Evacanthinae were sister groups with high nodal support.

Tick mitochondrial genomes: structural characteristics and phylogenetic implications

Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.

The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis

The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.

The Complete Mitochondrial Genome of Ugyops sp. (Hemiptera: Delphacidae)

The complete mitochondrial genome (mitogenome) of Ugyops sp. (Hemiptera: Delphacidae) was sequenced, making it the first determined mitogenome from the subfamily Asiracinae, the basal clade of the family Delphacidae. The mitogenome was 15,259 bp in length with A + T content of 77.65% and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. The gene order was identical with that of the ancestral insect. The nucleotide composition analysis indicated that the whole mitogenome was strongly A-skewed (0.288) and highly C-skewed (-0.270). For PCGs on the J-strand, the AT skew was positive, and the GC skew was negative. All PCGs started with canonical ATN codons, except for cox1 and nad5, which used CTG and GTG as start codon, respectively. All tRNAs could fold into typical cloverleaf secondary structures, with the exception of trnS1 (AGN), in which the dihydrouridine arm was reduced to a simple loop. The control region included a poly-T stretch downstream of the small rRNA gene (rrnS), a subregion of higher A + T content and tandemly repeated sequence near trnI. The mitogenome of Ugyops sp. could be very helpful in exploring the diversity and evolution of mitogenomes in Delphacidae.