The complete mitochondrial genome of Diaphorina citri (Hemiptera: Psyllidae) and phylogenetic analysis

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is the most serious pest of citrus as the vector of Huanglongbing (HLB), the citrus greening disease. In this study, the complete mitochondrial genome (mitogenome) of D. citri has been sequenced and annotated, and a comparative analysis is provided with known Psylloidea species. The mitogenome of D. citri is a typical circular molecular of 15,038 bp in length with an A + T content of 74.56%, contains the typical 37 genes and the gene order is identical to the other Psylloidea mitogenomes. The nucleotide composition and codon usage of D. citri are similar to the four Psylloidea species. All protein-coding genes (PCGs) use standard initiation codons (TAN), stop with TAA and TAG except ND2 and ND5 which stop with incomplete termination codon T. All tRNAs have the typical clover-leaf structure, with the exception of trnS1 lacking the dihydrouridine (DHU) arm. The control region is located between rrnL and the trnI gene with the highest A + T content among the five Psylloidea species. Phylogenetic analysis is conducted based on the 13 PCGs or/and 2 rRNAs of 23 Sternorrhycha mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) analysis suggest a clear relationship of Psylloidea, Aleyrodoidea and Aphidoidea within Sternorrhycha, which support the traditional morphological classification.     

Characterization of the complete mitochondrial genome of Drawida gisti (Metagynophora,Moniligastridae) and comparison with other Metagynophora species

Here, the complete mitochondrial genome (mitogenome) of Drawida gisti was sequenced and compared with the mitogenomes of other Metagynophora species. The circular mitogenome was 14,648 bp in length and contained two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The types of constitutive genes and the direction of the coding strand that appeared in Drawida mitogenome were identical to those observed in other Metagynophora species, except for a missing lengthy non-coding region. The conservative relationships between Drawida species were supported by the overall analyses of 13 PCGs, two rRNAs, and 22 tRNAs. A comparison of the Metagynophora mitogenomes revealed that the ATP8 gene possessed the highest polymorphism among the 13 PCGs and two rRNAs. Phylogenetic analysis suggested that the Moniligastridae contained Drawida, which is a primitive Metagynophora group. Our study provides a step forward toward elucidating the evolutionary linkages within Drawida and even Metagynophora.     

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera,Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis

The mitochondrial genome (mitogenome) can help us understand the phylogenetic relationships within the genus Lethe and the subfamily Satyrinae. In this study, we sequenced the complete mitogenomes of 14 Lethe species, which range in size from 15,225 to 15,271 bp, with both 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and a noncoding A + T-rich region. The gene arrangement and orientation is similar to typical mitogenomes of Lepidoptera. The Ka/Ks ratio shows that cox1 has the slowest evolutionary rate. The secondary structure of trnN lacks the Pseudouracil loop (TψC loop) in most Lethe species. The inferred phylogenetic analyses show that Lethe is a well-supported monophyletic group, and reveal 2 major clades within the genus Lethe, which is consistent with previous morphological classifications.     

The complete nucleotide sequence of the mitochondrial genome of <Emphasis Type="Italic">Phthonandria atrilineata</Emphasis> (Lepidoptera: Geometridae)

Using long-polymerase chain reaction (Long-PCR) method, we determined the complete nucleotide sequence of the mitochondrial genome (mitogenome) of Phthonandria atrilineata. The complete mtDNA from P. atrilineata was 15,499 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The P. atrilineata genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. The nucleotide composition of P. atrilineata mitogenome was biased toward A + T nucleotides (81.02%), and the 13 PCGs show different A + T contents that range from 73.25% (cox1) to 92.12% (atp8). Phthonandria had the canonical set of 22 tRNA genes, that fold in the typical cloverleaf structure described for metazoan mt tRNAs, with the unique exception of trnS(AGN). The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, which confirmed that P. atrilineata is most closely related to the superfamily Bombycoidea.     

The complete mitochondrial genome of the butterfly <Emphasis Type="Italic">Apatura metis</Emphasis> (Lepidoptera: Nymphalidae)

As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer’s purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA ^Ser(AGN) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif ‘ATAGA’ and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.     

Characterization of the complete mitochondrial genome of Diaphania pyloalis (Lepidoptera: Pyralididae)

The complete mitochondrial genome (mitogenome) of Diaphania pyloalis (Lepidoptera: Pyralididae) was determined to be 15,298 bp and has the typical gene organization of mitogenomes from lepidopteran insects. It consists of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The A + T content of this mitogenome is 80.83% and the AT skew is slightly positive. All PCGs are initiated by ATN codons, except for cytochrome c oxidase subunit 1 (cox1) gene which is initiated by CGA. Only the cox2 gene has an incomplete stop codon consisting of just a T. All the tRNA genes display a typical clover-leaf structure of mitochondrial tRNA. The A + T-rich region of the mitogenome is 332 bp in length, including several common features found in lepidopteran mitogenomes. Phylogenetic analysis showed that the D. pyloalis is close to Pyralididae.     

The complete mitochondrial genomes of two vent squat lobsters,Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications

Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication–random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.     

Complete mitochondrial genomes of Conogethes punctiferalis and C. pinicolalis (Lepidoptera: Crambidae): Genomic comparison and phylogenetic inference in Pyraloidea

Conogethes punctiferalis Guenée, 1854 (Lepidoptera: Crambidae) is a serious polyphagous pest that attacks more than one hundred species of plants. Previously, C. punctiferalis was determined to be composed of two ecotypes; later, Conogethes pinicolalis, was described as a separate species. Due to the prolonged negligence of C. pinicolalis as an independent species, the genetic perspective of the two species is limited. Thus, in this study, 15,332 and 15,336 bp-long complete mitochondrial genome (mitogenome) of the two species were sequenced and compared to each other and to 54 available mitogenomes of Pyraloidea. The comparison of each protein-coding gene (PCG) and rRNA gene of the two congeneric species showed substantial sequence divergence, ranging from 3.13% (ATP8) to 8.3% (COIII), with an average of 5.92%. Phylogenetic analyses using concatenated sequences of 13 PCGs and 2 rRNAs (12,458 bp including gaps), both by maximum likelihood (ML) and Bayesian inference (BI) methods, consistently supported the monophyly of each family (Crambidae and Pyralidae) and subfamily, generally with the highest nodal supports. The subfamilial relationships of ((((Acentropinae + Schoenobiinae) + (Scopariinae + Crambinae)) + Evergestinae) + (Spilomelinae + Pyraustinae)) in Crambidae and the subfamilial relationships of ((((Pyralinae + Epipaschiinae) + Phycitinae) + Galleriilinae)) in Pyralidae were obtained in both analyses. However, nodal supports were substantially low in this study, mainly due to limited taxa.     

The first complete mitochondrial genome of the Indian Tent Turtle,Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next‐generation sequencing. This denovo assembly encodes 37 genes: 13 protein‐coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with “GTG” and NADH dehydrogenase subunit 5 with “ATA.” The termination codons, “TAA” and “AGA” were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3′ end of CR. Further, two copies of a unique tandem repeat “TTCTCTTT” were identified in P. tentoria. The Bayesian and maximum‐likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in‐depth phylogenetic and evolutionary relationships.     

Complete mitochondrial genome of the hemp borer,Grapholita delineana (Lepidoptera: Tortricidae): Gene variability and phylogeny among Grapholita

The mitochondrial genome (mitogenome) has been extensively used in phylogenetics and species-level evolutionary investigations. The lepidopteran family Tortricidae (leaf-roller moths), including the genus Grapholita, contains numerous species of economic importance, but for the majority of Grapholita species, their mitogenomes remain poorly studied. Here, we sequence and annotate the full mitogenome of Grapholita delineana, an important pest of hemp worldwide and compare it with the mitogenomes of two congeneric species available from GenBank. The G. delineana mitogenome is 15,599 bp long, including 37 typical mitochondrial genes and an A + T-rich region. Gene content, order and orientation are identical to other reported tortricid mitogenomes. Analyses of nucleotide diversity, Ka/Ks, genetic distance and number of variable sites together suggest that nad6 is the fastest-evolving gene among the mitochondrial PCGs of Grapholita. Our analyses indicate that Grapholita, as presently defined, is not monophyletic, confirming previous morphological and multiple-gene studies, using mitogenomic evidence. Our study provides information on comparative mitogenomics of Tortricidae especially Grapholita.     

The complete mitochondrial genome of Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) and comparison with other Brachyuran crabs

Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR). The control region spanns 420 bp. The genome composition was highly A+T biased 75.60% and showed negative AT-skew (−0.03) and negative GC-skew (−0.47). Compared with the ancestor of Brachyura, the gene order of Sesarmidae has several differences and the gene order of P. pictum is typical for mitogenomes of Sesarmidae. Phylogenetic tree based on nucleotide sequences of mitochondrial 13 PCGs using BI and ML determined that P. pictum has a sister group relationship with Parasesarma tripectinis and belongs to Sesarmidae.     

Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications

The mitochondrial genome is now widely used in the study of phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate, and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomic level, we sequenced and annotated the complete mitogenomes of 3 skippers: Ampittia virgata, Halpe nephele, and Onryza maga (new mitogenomes for 2 genera) with a total length of 15,333 bp, 15,291 bp, and 15,381 bp, respectively. The mitogenomes all contain 13 protein‐coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a noncoding A + T‐rich region and are consistent with other lepidopterans in gene order and type. In addition, we reconstructed the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the tribe Aeromachini in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + (Pyrginae + ((Eudaminae + Tagiadinae) + (Heteropterinae + ((Trapezitinae + Barcinae) + Hesperiinae))))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.     

The complete mitochondrial genome of Pardosa pusiola (Araneae,Lycosidae) and its phylogenetic implications

The mitochondrial genome (mitogenome) is useful for identification and phylogenetic analyses among arthropods, but there are no sufficient mitogenome data for wolf spiders. To enrich the mitogenome database of wolf spiders, the complete mitogenome of Pardosa pusiola was sequenced by high-throughput sequencing. It is 14,284 bp, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). It represents a high bias toward A and T nucleotides with an A + T content of 76.49%. The mitogenome exhibited a negative AT skew (−0.13) and a positive GC skew (0.32). Most PCGs started with ATN codons and ended with TAA, TAG, or an incomplete T. In addition, most tRNAs had aberrant secondary structures with the absence of DHU arm or TΨC arm. Analysis performed with CREx software demonstrated that large-scale rearrangements of tRNAs were observed in the mitogenome of P. pusiola as compared with the putative ancestral mitogenome. The Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees based on the 13 PCGs of 25 spiders had the same topology, which could be presented as (Araneidae + (Agelenidae + (Dictynidae + Desidae)) + (Salticidae + (Thomisidae + (Oxyopidae + (Pisauridae + Lycosidae))))). This study offers a useful genetic resource for the taxonomy and phylogeny of spiders.     

Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae,Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae

To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein‐coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in noncoding regions. Our results showed the first case of intraspecific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae.     

The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura

In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (−0.010) and GC-skew (−0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.     

Genetic diversity of genus Vespa including an invaded species of V. velutina (Hymenoptera: Vespidae) in Korea inferred from DNA barcoding data

With about 5000 known species, the Vespidae is a large family belongs to order Hymenoptera. The genus Vespa with 22 species is one of the four genera of the subfamily Vespinae. In Korea, 10 species and subspecies are recognized. Because of their social behavior, their treat to human health and their impact in apiculture, the reliable and sometimes automated identification of these insects to species level are important. To test the efficacy of DNA barcoding method for identification of species of the genus Vespa in Korea, 30 samples of eight Korean species of genus Vespa were collected and mitochondrial DNAs of 658 bp fragment cytochrome oxidase subunit 1 (CO1) region were sequenced. A Bayesian Inference based on COI gene of the Korean Vespa species was constructed. The phylogenetic tree shoed that identification of all specimens is possible based on COI gene and we found strong relation between the sequences of the collected species from different localities in South Korea which clustered together with 100% support with sequences of the same species in GenBank. The results demonstrate that DNA barcoding is a useful technique for rapid and accurate species recognition in Korean Vespa species. The DNA barcode part of COI for V. binghami is provided for the first time that can help for identification of this species through DNA barcoding. Also, the genetic diversity among Korean Vespa velutina was zero suggests that the invasion might have occurred in a single event with small number of founders.     

Complete mitochondrial genome of the wild silkmoth,Saturnia boisduvalii (Lepidoptera: Saturniidae)

We sequenced mitochondrial genome (mitogenome) of the wild silkmoth, Saturnia boisduvalii (Lepidoptera: Saturniidae), which occurs in mainland Korea, and compared it with other species in Bombycoidea to characterize the genomic evolution of the superfamily. We found that the composition and arrangement of genes in the 15,257‐bp S. boisduvalii genome are typical of the majority of Lepidoptera, and the genome is biased toward A/T nucleotides, as previously reported. Comparison of individual gene divergence among bombycoid species showed that ND6 was most variable (p‐distance = 0.21), whereas COI and COII were most conserved, indicating that of all the protein‐coding genes (PCGs) ND6 appear to have evolved most rapidly. Thus, other PCGs beside COI are potential alternative markers, where scrutinized discrimination among species is required.     

The complete mitochondrial genome of Plesiastrea versipora (Scleractinia,Plesiastreidae) sheds light on its phylogeny and taxonomy of the family Plesiastreidae

The genus Plesiastrea used to be a member of the traditional family Faviidae, falling into the challenging ‘Bigmessidae’ clade, and was re-established until recent molecular phylogenies published. The entire mitogenome of the symbiotic coral Plesiastrea versipora (Lamarck, 1816), the type species of the family Plesiastreidae, was sequenced. The length of the mitochondrial genome is 15,320 bp and it includes thirteen protein-coding genes (PCGs), two rRNAs and two tRNAs. The nucleotide composition of GC is 32%. We perform phylogenetic reconstruction based on maximum likelihood (ML) and Bayesian analysis(BI) using all PCGs. Our result indicates that P. versipora clusters closely with species which belong to Mussidae, Merulinidae and Lobophylliidae. Our phylogenetic analyses provide solid evidence for phylogenetic placement of P. versipora and the evolutionary relationships among different families within the traditional robust clade of Scleractinia. In addition, the mitogenome data provide useful information for further molecular systematic investigations on Plesiastreidae as well as conservation biology research of P. versipora.     

First record of occurrence of Xenos moutoni (Strepsiptera; Stylopidae), an important parasite of hornets (Hymenoptera: Vespidae: Vespa), in Korea

This is the first record of Xenos moutoni, a specialized parasite of hornets (Vespa spp.), in Korea. Among six Vespa species collected with bait traps in Andong, central South Korea, approximately 10% of female Vespa analis (gynes plus workers) were parasitized, whereas the other five species (V. crabro, V. mandarinia, V. simillima, V. ducalis, and V. dybowskii) were not. Almost all parasitized hornets had a single female parasite in the gaster.