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 genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

The complete mitochondrial genome of Biston panterinaria (Lepidoptera: Geometridae), with phylogenetic utility of mitochondrial genome in the Lepidoptera

The complete mitochondrial genome (mitogenome) of the Chinese pistacia looper Biston panterinaria was sequenced and annotated (15,517 bp). It contains the typical 37 genes of animal mitogenomes and a high A + T content (79.5%). All protein coding genes (PCGs) use standard ATN initiation codons except for cytochrome c oxidase 1 (COX1) with CGA. Eleven PCGs use a common stop codon of TAA or TAG, whereas COX2 and NADH dehydrogenase 4 (ND4) use a single T. All transfer RNA (tRNA) genes have the typical clover-leaf structure with the exception of tRNA^Ser(AGN). We reconstructed a preliminary mitochondrial phylogeny of six ditrysian superfamilies and performed comparative analyses of inference methods (Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP)), dataset compositions (including and excluding 3rd codon positions), and alignment methods (Muscle, Clustal W, and MAFFT). Our analyses indicated that inference methods and dataset compositions more significantly affected the phylogenetic results than alignment methods. BI analysis consistently revealed uncontroversial relationships with all dataset compositions. By contrast, ML analysis failed to reconstruct stable phylogeny at two nodes, whereas MP analysis had more difficulties in the tree resolution and nodal support. Distinct from most previous studies, our analyses revealed that Geometroidea had a closer lineage relationship with Bombycoidea than Noctuoidea. Similar to previous molecular studies, our analyses revealed that Hesperiidae were nested in the Papilionoidea clade, providing further evidence to the previous concept that Papilionoidea was paraphyletic, and none of the butterflies were associated with the Macroheterocera.     

A mitogenomic phylogeny and genetic history of sable (Martes zibellina)

We assessed phylogeny of sable (Martes zibellina, Linnaeus, 1758) by sequence analysis of nearly complete, new mitochondrial genomes in 36 specimens from different localities in northern Eurasia (Primorye, Khabarovsk and Krasnoyarsk regions, the Kamchatka Peninsula, the Kuril Islands and the Urals). Phylogenetic analysis of mtDNA sequences demonstrates that two clades, A and BC, radiated about 200–300 thousand years ago (kya) according to results of Bayesian molecular clock and RelTime analyses of different mitogenome alignments (nearly complete mtDNA sequences, protein-coding region, and synonymous sites), while the age estimates of clades A, B and C fall within the Late Pleistocene (~ 50–140 kya). Bayesian skyline plots (BSPs) of sable population size change based on analysis of nearly complete mtDNAs show an expansion around 40 kya in the warm Karganian time, without a decline of population size around the Last Glacial Maximum (21 kya). The BSPs based on synonymous clock rate indicate that M. zibellina experienced demographic expansions later, approximately 22 kya. The A2a clade that colonized Kamchatka ~ 23–50 kya (depending on the mutation rate used) survived the last glaciation there as demonstrated by the BSP analysis. In addition, we have found evidence of positive selection acting at ND4 and cytochrome b genes, thereby suggesting adaptive evolution of the A2a clade in Kamchatka.     

The complete mitochondrial genome sequence of the world's largest fish,the whale shark (Rhincodon typus), and its comparison with those of related shark species

The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a “vulnerable” species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes it an important species for conservation efforts. We report here the first complete sequence of the mitochondrial genome (mitogenome) of the whale shark obtained by next-generation sequencing methods. The assembled mitogenome is a 16,875 bp circle, comprising of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. We also performed comparative analysis of the whale shark mitogenome to the available mitogenome sequences of 17 other shark species, four from the order Orectolobiformes, five from Lamniformes and eight from Carcharhiniformes. The nucleotide composition, number and arrangement of the genes in whale shark mitogenome are the same as found in the mitogenomes of the other members of the order Orectolobiformes and its closest orders Lamniformes and Carcharhiniformes, although the whale shark mitogenome had a slightly longer control region. The availability of mitogenome sequence of whale shark will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this species.     

The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids

To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A + T content (84.76%) and strong C skew (− 0.26) was arranged in the same gene order as that of the ancestral insect. Unlike typical insect mitogenomes, D. noxia possessed a large tandem repeat region (644 bp) located between trnE and trnF. Sequencing partial mitogenome of the cotton aphid (Aphis gossypii) further confirmed the presence of the large repeat region in aphids, but with different repeat length and copy number. Another motif (58 bp) tandemly repeated 2.3 times in the control region of D. noxia. All repeat units in D. noxia could be folded into stem-loop secondary structures, which could further promote an increase in copy numbers. Characterization of the D. noxia mitogenome revealed distinct mitogenome architectures, thus advancing our understanding of insect mitogenomic diversities and evolution.     

The phylogeny of Ephemeroptera in Pterygota revealed by the mitochondrial genome of Siphluriscus chinensis (Hexapoda: Insecta)

The mayfly species Siphluriscus chinensis (Siphluriscidae) has valuable structures useful for phylogeny reconstruction, given its putative basal position within the Ephemeroptera. Here its nearly complete mitochondrial genome is sequenced. We built phylogenetic trees through multiple analytical strategies with some other insect mitogenomes. Structurally, the obtained mitochondrial genome of S. chinensis is 16,616 bp in length, ¹ containing 37 genes and an extra trnK-like (trnK2 (AAA)) gene. The 12 PCGs start with typical ATN codons, except the nad1 gene which starts with an unnormalized TTG. Like other known mayfly mitogenomes, the strand bias has negative AT-skew and negative GC-skew. Phylogenetically, our topologies suggest that Odonata is the basally diverged clade in Pterygota; Ephemeroptera is the sister group of the Neoptera; and S. chinensis is indeed the most basal mayfly branch.     

The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae)

The complete mitogenomes of Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis are 15,660 bp, 15,657 bp and 15,661 bp in size, respectively. All three mitogenomes contain a standard set of 13 protein - coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T-rich region in the same order as those of the other analysed caeliferan species, including the rearrangement of trnAsp and trnLys. The putative initiation codon for the cox1 gene in the three species is CCG. The long polythymine stretch (T-stretch) in the A + T-rich region of the three species is not adjacent to the trnIle but inside the stem–loop sequence in the majority strand. The mitogenomes of F. helanshanensis and P. rubimarginis have higher overall similarities. The characterization of the three mitogenomes will enrich our knowledge on the Pamphagidae mitogenome. The phylogenetic analyses indicated that within the Caelifera, Pyrgomorphoidea is a sister group to Acridoidea. The species from the Pamphagidae form a monophyletic group, as is the case for Acrididae. Furthermore, the two families cluster as sister groups, supporting the monophyly of Acridoidea. The relationships among eight acridid subfamilies were (Cyrtacanthacridinae + (Calliptaminae + (Catantopinae + (Oxyinae + (Melanopline + (Acridinae + (Oedipodinae + Gomphocerinae))))))).     

Characterization of the complete mitogenome of Trachylophus sinensis (Coleoptera: Cerambycidae: Cerambycinae), the type species of Trachylophus and its phylogenetic implications

Complete mitochondrial genomes (mitogenomes) have long been proved as reliable markers for phylogenetic reconstruction among diverse animal groups, especially benefited from recent rapid development of sequencing techniques. However, the mitogenomes of many important clades remain poorly represented, which restricted the understanding of macroscale evolutionary history of these groups. Here, we sequenced and characterized the complete mitogenome of Trachylophus sinensis, a type species of the Trachylophus genus, which also represents the first sequenced mitogenome in this genus. The complete circular mitogenome was 15,746 bp in length, containing 37 typical genes and one noncoding AT-rich control region. The nucleotide composition of the mitogenome was highly A + T biased, accounting for 70.07 % of the whole mitogenome with a slightly positive AT skewness (0.106). The 13 Protein coding genes (PCGs) used ATN as their start codons, except nad1 which used TTG. All tRNA genes were predicted with a characteristic cloverleaf secondary structure except trnS1^(AGN), whose dihydrouridine (DHU) arm was replaced by a simple loop. Phylogenetic analyses recovered Cerambycinae as a monophyletic group with high node supports and the sister relationship between T. sinensis and Nadezhdiella cantori. However, we found that deeper nodes showed not strong support, which may be caused by limited taxa sampling in our study. More mitogenomes should be sequenced representing various taxonomic levels, especially closely related species, which will enhance our understanding of phylogenetic relationships among Cerambycinae.     

Contribution to the mitogenome diversity in Delphacinae: Phylogenetic and ecological implications

We document the complete (or nearly complete) mitogenomes of 20 Delphacidae taxa, and together with 17 other delphacid mitogenomes currently in GenBank, to reconstruct the phylogeny of the Delphacinae and to investigate mitogenome differences among members of Delphacini, Tropidocephalini and Saccharosydnini. The mitogenomes of the 20 species encode the complete set of 37 genes usually found in animal mitogenomes. The length of complete mitogenomes in Delphacinae ranges from 15,531 to 16,231 bp. The gene order of all newly sequenced mitogenomes are identical, and the mitogenome gene order of Stenocranus matsumurai Metcalf in Stenocraninae has a transposition of tRNA^Thr. The two-clade system in Tropidocephalini was supported with high value (PP = 1, BS = 100), and the monophyly of Bambusiphaga was recovered in this study. Finally, we found that the host shift from plants with a C₃ to a C₄ photosynthetic pathway appears to have occurred independently in several clades.     

Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae

The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus + Collichthys lucidus and Larimichthys crocea + Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.     

The complete mitochondrial genome of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae)

The complete nucleotide sequence of the mitochondrial genome (mitogenome) of Gomphocerus tibetanus Uvarov, 1935 (Orthoptera: Acrididae: Gomphocerinae) was determined. It is 15,571 bp in length and contains 74.8% A + T. All Gomphocerus tibetanus protein-coding sequences start with a typical ATN codon. The usual termination codons (TAA and TAG) were found from 13 PCGs except COI and COII which took incomplete codon T as termination codons. All tRNA genes could be folded into the typical cloverleaf secondary structure, except tRNA^Ser(AGN) lacking of dihydrouridine (D) arm. The sizes of the large and small ribosomal RNA genes are 1313 and 822 bp, respectively. The A + T content of the A + T-rich region is 82.3%. A preliminary analysis on characteristics of Gomphocerinae mitogenome was made by comparision among three Gomphocerinae mitogenomes and Locusta migratoria.     

Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics

Phodopus roborovskii (subfamily Cricetinae) is widely distributed in the northern arid regions of China. This study reports its complete mitochondrial genome (mitogenome) for the first time. The complete sequence was 16,273 bp long, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. The base composition and codon usage were described. The putative origin of replication for the light strand (O_L) of P. roborovskii was approximately 45 bp long and was highly conserved in the stem-loop and adjacent sequences, but the starting sequence of replication varied between genera among Rodentia. We analyzed the three domains of the D-loop region, and the results indicated that the central domain had higher G + C content and lower A + T content than two peripheral domains. Phylogenetic analyses indicated high resolution in four main divergent clades using mitogenomes data within Cricetidae. Within Cricetinae clade, P. roborovskii was at basal position which was in line with previous researches, and it shared a common ancestor with other extant hamsters. This work validated previous molecular and karyotype researches using mitogenomes data, and provided a set of useful data on phylogeny and molecular evolution in Cricetidae species.     

The mitochondrial genome of Gatzara jezoensis (Neuroptera: Myrmeleontidae) and phylogenetic analysis of Neuroptera

Phylogenetic relationship within Neuroptera is controversial, particularly for the various hypotheses based on both morphological and molecular evidence. In the present study, we determined the complete mitochondrial genome (mitogenome) of Gatzara jezoensis, which is the second representative of the tribe Dendroleontini. The G. jezoensis mitogenome contained the conserved set of 37 mitochondrial genes and a putative control region, with a conserved gene arrangement which was similar to that of most sequenced neuropteran mitogenomes. All transfer RNAs exhibited the canonical cloverleaf secondary structure, except for trnS^(AGN). The control region contained two conserved elements (ploy-T stretch and ATGGTTCAAYAAAATAAYYCYCTC motif) and abundant microsatellite-like elements. The phylogenetic analysis of sequenced neuropteran mitogenomes using the concatenated protein-coding genes (PCGs) and ribosomal genes recovered the monophyly of Myrmeleontidae, which revealed this dataset could generate the more robust phylogeny of Neuroptera than that of 13 PCGs dataset.     

The mitochondrial genome of the Kentish Plover <Emphasis Type="Italic">Charadrius alexandrinus</Emphasis> (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii

The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii’s mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD?=?182, n?=?11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.     

Next‐generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.)

Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next‐generation sequencing methods, it is now feasible to efficiently sequence mitogenomes of large numbers of individuals once a reference mitogenome is available. However, assembling the initial mitogenomes of nonmodel organisms can present challenges, for example, in birds, where mtDNA is often subject to gene rearrangements and duplications. We developed a workflow based on Illumina paired‐end, whole‐genome shotgun sequencing, which we used to generate complete 19‐kilobase mitogenomes for each of three species of North Pacific albatross, a group of birds known to carry a tandem duplication. Although this duplication had been described previously, our procedure did not depend on this prior knowledge, nor did it require a closely related reference mitogenome (e.g. a mammalian mitogenome was sufficient). We employed an iterative process including de novo assembly, reference‐guided assembly and gap closing, which enabled us to detect duplications, determine gene order and identify sequence for primer positioning to resolve any mitogenome ambiguity (via minimal targeted Sanger sequencing). We present full mtDNA annotations, including 22 tRNAs, 2 rRNAs, 13 protein‐coding genes, a control region and a duplicated feature for all three species. Pairwise comparisons supported previous hypotheses regarding the phylogenetic relationships within this group and occurrence of a shared tandem duplication. The resulting mitogenome sequences will enable rapid, high‐throughput NGS mitogenome sequencing of North Pacific albatrosses via direct reference‐guided assembly. Moreover, our approach to assembling mitogenomes should be applicable to any taxon.     

Complete mitochondrial genome of the Iberian Mole <Emphasis Type="Italic">Talpa occidentalis</Emphasis> (Talpidae,Insectivora) and comparison with <Emphasis Type="Italic">Talpa europaea</Emphasis>

The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.     

Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes

Two novel mitogenomes of Eozapus setchuanus (KJ648495) and Sicista concolor (KJ648496) were reported and their total lengths were 16,630 bp and 16,493 bp, respectively. Both mitogenomes which were analogous to other rodent mitogenomes, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Specifically, the ND2 gene of S. concolor has three amino acids lesser than that of two other Dipodidae species (E. setchuanus and Jaculus jaculus) due to a premature termination codon in the 3′ end. We detected a tandem repeat cluster of 221 bp and 274 bp in the control region of S. concolor and E. setchuanus, respectively. Along with phylogenetic relationship analysis, we speculated that the tandem repeats in control regions might be common in Dipodinae species. Our phylogenetic analysis using concatenated mitochondrial gene datasets suggested five suborder and 16 family monophyletic groups in 54 rodent taxa sampled and strongly supported a basal position of the squirrel-related clade (PP = 1; BP = 100). Dipodidae had a sister-group relationship with Muroidea, and Sicistinae was in the base of Dipodidae clade. The complete mitochondrial genomes showed high resolution in deep-level phylogenetic relationship reconstructions of Rodentia.