Complete mitochondrial genome of the Korean endemic springtail Tomocerus caputiviolaceus Lee 1975 (Collembola: Tomoceridae)

The complete mitochondrial genome of Tomocerus caputiviolaceus was sequenced and assembled. The complete mitochondrial genome is 15,519 bp in length. The mitogenome contained 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. In phylogenetic analysis based on the nucleotide sequences of 13 PCGs, T. caputiviolaceus is closely related to Tomocerus qinae Yu, Yao & Hu, 2016, both of which belong to the genus Tomocerus within the family Tomoceridae.

A report on the complete mitochondrial genome of the trematode Azygia robusta Odhner, 1911, its new definitive host from the Russian Far East, and unexpected phylogeny of Azygiidae within Digenea, as inferred from mitogenome sequences

New data on the complete mitochondrial genome of Azygia robusta (Azygiidae) were obtained by the next-generation sequencing (NGS) approach. The mitochondrial DNA (mtDNA) of A. robusta had a length of 13 857 bp and included 12 protein-coding genes, two ribosomal genes, 22 transfer RNA genes, and two non-coding regions. The nucleotide sequences of the complete mitochondrial genomes of two A. robusta specimens differed from each other by 0.12 ± 0.03%. Six of 12 protein-coding genes demonstrated intraspecific variation. The difference between the nucleotide sequences of the complete mitochondrial genomes of A. robusta and Azygia hwangtsiyui was 26.95 ± 0.35%; the interspecific variation of protein-coding genes between A. robusta and A. hwangtsiyui ranged from 20.5 ± 0.9% (cox1) to 30.7 ± 1.2% (nad5). The observed gene arrangement in the mtDNA sequence of A. robusta was identical to that of A. hwangtsiyui. Codon usage and amino acid frequencies were highly similar between A. robusta and A. hwangtsiyui. The results of phylogenetic analyses based on mtDNA protein-coding regions showed that A. robusta is closely related to A. hwangtsiyui (belonging to the same suborder, Azygiida) that formed a distinct early-diverging branch relative to all other Digenea. A preliminary morphological analysis of paratypes of the two azygiid specimens studied showed visible morphological differences between them. The specimen extracted from Sakhalin taimen (Parahucho perryi) was most similar to A. robusta. Thus, we here provide the first record of a new definitive host, P. perryi, for A. robusta and also molecular characteristics of the trematode specimens.

The complete mitochondrial genome of Spurilla braziliana MacFarland 1909 (Nudibranchia, Aeolidiidae)

Spurilla braziliana MacFarland 1909 is a morphologically diverse nudibranch found in the Pacific and Western Atlantic. The complete mitochondrial genome of S. braziliana has been constructed using next-generation sequencing technology. The mitochondrial genome is 14,291 bp and contains 13 protein-coding genes, 2 rRNA genes, and 23 tRNA genes. Molecular phylogenetic analysis using the maximum likelihood method revealed that S. braziliana is included in the superfamily Aeolidioidea and forms a monophyletic group with Berghia stephanieae, a nudibranch of the family Aeolidiidae. This study reinforces existing taxonomic insights and provides a basis for further molecular phylogenetic analysis.

The complete mitochondrial genome of Choristoneura metasequoiacola Liu,1983 (Lepidoptera: Tortricidae)

Choristoneura metasequoiacola Liu, 1983 is an important caterpillar species that specifically infests the leaves and branches of Metasequoia glyptostroboides Hu & W. C. Cheng 1948 with short larval infestations, long-term dormancy, and has a limited distribution in Lichuan, Hubei, China. The complete mitochondria genome of C. metasequoiacola was determined by using Illumina NovaSeq, and analyzed based on previously annotated sibling species. In total, we obtained mitochondria genome with 15,128 bp in length, circular in shape with a double-stranded closed ring structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and an AT-rich region. Of which the nucleotide composition was highly A + T biased, accounting for 81.98% of the whole mitogenome. Thirteen protein-coding genes (PCGs) were 11,142 bp; Twenty-two tRNA genes and AT-rich region were 1,472 and 199 bp, respectively. Phylogenetically, the relationship between Choristoneura spp. (containing C. metasequoiacola) and Adoxophyes spp. was closer than any other two genera from Tortricidae, and the relationship between C. metasequoiacola and C.murinana was the closest among nine sibling species from that genus, which helps to explain species evolution within the family Tortricidae.

Characterization of the complete mitochondrial genome and phylogenetic analysis of Epiverta chelonia (Coleoptera: Coccinellidae)

Epiverta chelonia (Mader 1933; Coleoptera: Coccinellidae) is an important economically and scientifically valuable insect. In this study, the first complete mitochondrial genome of E. chelonia was sequenced and characterized using next-generation sequencing techniques. The circular mitogenome of E. chelonia consists of 17,347 bp including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop). The base composition was AT-biased (75.77%). Bayesian Inference and Maximum likelihood phylogenetic trees strongly supported the monophyly of Coccinellinae. Also, E. chelonia was supported as the sister group of Subcoccinella vigintiquatuorpunctata, within Epilachninae. Thus, the E. chelonia mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich family Coccinellidae of Coleoptera.

Complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata: Macromiidae)

We describe the first time sequencing and assembly of the complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata; Macromiidae; Macromia). The mitochondrial genome of M. manchurica was found to be 15,560 bp. It contains thirteen protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and AT-rich region. The overall base composition of A. japonicus is A-38.6%, C-17.0%, G-12.5%, and T-31.9%. A phylogenetic analysis of 14 species within the order Odonata and order Ephemeroptera suggested that Macromia amphigena is most closely related to M. manchurica.

Characterization of Seventeen Complete Mitochondrial Genomes: Structural Features and Phylogenetic Implications of the Lepidopteran Insects

Lepidoptera (moths and butterflies) are widely distributed in the world, but high-level phylogeny in Lepidoptera remains uncertain. More mitochondrial genome (mitogenome) data can help to conduct comprehensive analysis and construct a robust phylogenetic tree. Here, we sequenced and annotated 17 complete moth mitogenomes and made comparative analysis with other moths. The gene order of trnM-trnI-trnQ in 17 moths was different from trnI-trnQ-trnM of ancestral insects. The number, type, and order of genes were consistent with reported moths. The length of newly sequenced complete mitogenomes ranged from 14,231 bp of Rhagastis albomarginatus to 15,756 bp of Numenes albofascia. These moth mitogenomes were typically with high A+T contents varied from 76.0% to 81.7% and exhibited negative GC skews. Among 13 protein coding genes (PCGs), some unusual initiations and terminations were found in part of newly sequenced moth mitogenomes. Three conserved gene-overlapping regions and one conserved intergenic region were detected among 17 mitogenomes. The phylogenetic relationship of major superfamilies in Macroheterocera was as follows: (Bombycoidea + Lasiocampoidea) + ((Drepanoidea + Geometroidea) + Noctuoidea)), which was different from previous studies. Moreover, the topology of Noctuoidea as (Notodontidae + (Erebidae + Noctuidae)) was supported by high Bayesian posterior probabilities (BPP = 1.0) and bootstrapping values (BSV = 100). This study greatly enriched the mitogenome database of moth and strengthened the high-level phylogenetic relationships of Lepidoptera.

Characterization of the complete mitochondrial genome of a harvesting ant Messor structor (Hymenoptera: Formicidae: Myrmicinae)

Messor structor (Latreille, 1798) is a keystone ant species in the genus Messor (Formicidae: Myrmicinae). Here, we reported the complete mitochondrial genome of M. structor. The circular mitogenome of M. structor is 17628 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The base composition was AT-biased (84.07%). Phylogenetic analysis suggests that it is closely related to Aphaenogaster famelica. The mitochondrial genome of M. structor will be a good source for understanding molecular evolutionary studies of this species and related ant species.

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.

The complete mitochondrial genome of a planarian flatworm Girardia tigrina (Tricladida: Dugesiidae)

Girardia tigrina, a freshwater planarian species native to America and introduced to other continents, has been usually used as model organism in many research fields of biology. In this study, we determined the complete mitochondrial genome of G. tigrina using next-generation sequencing (NGS). The complete mitogenome was 15,938 bp in length, with 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and ATP8 was absent in the mitogenome of G. tigrina as in the mitogenomes of some other flatworms. The maximum-likelihood phylogenetic tree suggested that G. tigrina was closely related to genus Dugesia in the clade of Tricladida.

The complete mitochondrial genome of Indian Cuckoo Cuculus micropterus (Aves: Cuculiformes)

The Indian Cuckoo, Cuculus micropterus, belongs to the family Cuculidae. In this paper, we sequenced and analysized the complete mitochondrial genome of C. micropterus. The complete mitochondrial genome of C. micropterus is 17,541 bp in length, which was submitted to the NCBI database under the accession number MZ048030. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA is 33.2% for A, 24.2% for T, 29.8% for C, and 12.8% for G, with a GC content of 42.6%. In order to explore the molecular phylogenetics evolution of Cuculidae, the nucleotide sequence data of 13 PCGs of C. micropterus and other 11 Cuculiformes were used for the phylogenetic analysis. The result shows that C. micropterus is closely related to Cuculus canorus bakeri. The study contributes to illuminating the taxonomic status of C. micropterus, and may facilitate further investigation of the evolution of Cuculidae.

Complete mitochondrial genomes of two marine monogonont rotifer Brachionus manjavacas strains

The complete mitochondrial genomes of Brachionus manjavacas German strain were 10,721 bp (mitochondrial DNA I) and 12,274 bp (mitochondrial DNA II) in size, while the complete mitochondrial genomes of B. manjavacas Australian strain were 10,889 bp (mitochondrial DNA I) and 12,443 bp (mitochondrial DNA II) in size. Of 12 protein-coding genes (PCGs), 99.6% of amino acid sequences were identical between the two strains. Of 12 PCGs of both B. manjavacas strains, three genes (ND1, ATP6, and ND5) had incomplete stop codon T. Furthermore, ATA was the start codon for ND4, ND5, and CO3 genes, whereas that for other PCGs was ATG in both strains. The base compositions of 12 PCGs in the B. manjavacas strains were similar, indicating that the mitochondrial genome of the two strains was structurally conserved over evolution. The gene structure and its orientation of 12 PGCs of B. manjavacas strains were identical, as shown in other marine Brachionus rotifers and the freshwater Brachionus rotifers, while the freshwater rotifer B. calyciflorus had an additional cytochrome b gene in the mitochondrial DNA I.

An Investigation of the Variations in Complete Mitochondrial Genomes of Lingula anatina in the Western Pacific Region

Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.

Characterization of the complete mitochondrial genome of the moss, Myurella julacea (Schwägr.) Schimp. (Bryidae, Theliaceae)

The present study reports the complete mitochondrial genome of Myurella julacea (Schwägr.) Schimp. (GenBank accession number MT850126); the genome size was 104,979 bp. The gene arrangement was found to be similar to that in other bryophytes, and the genome consisted of 40 protein-coding genes (PCGs), 3 ribosomal RNAs (rRNAs), and 24 transfer RNAs (tRNAs). The phylogenic relationship was analyzed by construction of a phylogenetic tree based on the mitogenome of M. julacea and 25 other bryophytes publicly available in GenBank. The complete mitogenome of M. julacea is expected to provide insights into the evolution of species belonging to the order Hypnales.

Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (Insecta: Diptera: Calliphoridae)

In this study, the complete mitochondrial (mt) genome of the New Zealand parasitic blowfly Calliphora vicina (blue bottle blowfly) field strain NZ_CalVic_NP was generated using next-generation sequencing technology and annotated. The 16,518 bp mt genome consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a 1689 bp non-coding region, similar to the two other available C. vicina and most metazoan mt genomes. Phylogenetic analysis showed that C. vicina NZ_CalVic_NP forms a monophyletic cluster with the remaining three Calliphorinae species. The complete mt genome sequence of C. vicina NZ_CalVic_NP is a resource to facilitate future species- and strain-level identification research and investigations into the evolutionary provenance within the Calliphoridae.

The complete mitochondrial genome of the New Zealand parasitic blowfly Lucilia sericata (Insecta: Diptera: Calliphoridae)

In this study, the complete mitochondrial (mt) genome of the New Zealand parasitic blowfly Lucilia sericata (green bottle blowfly) field strain NZ_LucSer_NP was generated using next-generation sequencing technology. The length of complete the mt genome is 15,938 bp, with 39.4% A, 13.0% C, 9.3% G, and 38.2% T nucleotide distribution. The complete mt genome consists of 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a 1124 bp non-coding region, similar to most metazoan mt genomes. Phylogenetic analysis showed that L. sericata NZ_LucSer_NP forms a monophyletic cluster with the remaining six Lucilia species and the Calliphoridae are polyphyletic. This study provides the first complete mt genome sequence for a L. sericata blowfly species derived from New Zealand to facilitate species identification and phylogenetic analysis.

The complete mitochondrial genome sequences of Japanese earthworms Metaphire hilgendorfi and Amynthas yunoshimensis (Clitellata: Megascolecidae)

Many studies have reported the complete mitochondrial genome sequences of Chinese Megascolecidae earthworms, however, there have been no reports on sequences originating from Japanese Megascolecidae earthworms. In this study, we determined complete mitochondrial genome sequences of two Japanese earthworms belonging to the Pheretima complex within the Megascolecidae family. Metaphire hilgendorfi is one of the most common earthworms in Japan and Amynthas yunoshimensis was found to be morphologically similar to M. hilgendorfi. The complete mitochondrial genomes of M. hilgendorfi (15,186 bp; LC573968) and A. yunoshimensis (15,109 bp; LC573969) contained typical 13 protein coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogenetic analysis revealed that these two species were sister species. Therefore, our findings will further contribute to phylogenetic and genetic diversity analyses of Megascolecidae earthworms.

Complete Mitochondrial Genome of Trichuristrichiura from Macaca sylvanus and Papio papio

Trichuriasis is among the most prevalent worldwide parasitism caused by helminths. For many years, Trichuris spp. have been described with a relatively narrow range of both morphological and biometrical features. The use of the complete mitochondrial genome (mitogenome) is an alternative and powerful molecular method for inferring phylogenies. Here, we present an overview of the contributions of mitogenome for Trichuris spp. from human and non-human primates. In addition, we carry out structural and phylogenetic comparative analyses with genomes of Trichuris species available in public datasets. The complete mt genomes of Trichuris trichiura and Trichuris sp. from Macaca sylvanus and T. trichiura from Papio papio are 14,091 bp, 14,047 bp and 14,089 bp in length, respectively. The three mt genomes are circular and consist of 37 genes—13 PCGs (cox1–3, nad1–6, nad4L, atp6, atp8 and cob), 22 transfer RNA genes (tRNAs), and two rRNAs (rrnL and rrnS). The molecular evidence presented here supports the hypothesis that T. trichiura de M. sylvanus (TMF31) and T. trichiura de P. papio (TPM1) were similar but genetically different with respect to Trichuris sp. from macaques (TMM5). The phylogenetic study also supported the evolution of the different Trichuris species. In conclusion, we suggest the existence of two cryptic species parasitizing M. sylvanus.

Complete mitochondrial genome of a Korean endemic freshwater mussel Nodularia breviconcha (Bivalvia: Unionidae)

Mitochondrial genome sequences were first determined and analyzed for a Korean endemic freshwater mussel Nodularia breviconcha (synonym Nodularia douglasiae sinuolatus; Unionidae, Unionida, Bivalvia). The complete mitochondrial genome was 15,741 bp in length, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The overall GC content of mitochondrial genome for N. breviconcha was 34.3%. Phylogenetic analysis of 18 species within the family Unionidae suggested that Nodularia douglasiae is the most closely related to N. breviconcha. Our study will provide baseline, but important information for future research on ecological and genetic/genomic characteristics of this species.

The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing

Mitochondrial DNA (mtDNA), coupled with maternal inheritance and relatively high mutation rates, provides a pivotal way for us to investigate the formation histories of populations. The Hui minority with Islamic faith is one of the most widely distributed ethnic groups in China. However, the exploration of Hui's genetic architecture from the complete mitochondrial genome perspective has not been detected yet. Therefore, in this study, we employed the complete mitochondrial genomes of 98 healthy and unrelated individuals from Northwest China, as well as 99 previously published populations containing 7274 individuals from all over the world as reference data, to comprehensively dissect the matrilineal landscape of Hui group. Our results demonstrated that Hui group exhibited closer genetic relationships with Chinese Han populations from different regions, which was largely attributable to the widespread of haplogroups D4, D5, M7, B4, and F1 in these populations. The demographic expansion of Hui group might occur during the Late Pleistocene. Finally, we also found that Hui group might have gene exchanges with Uygur, Tibetan, and Tajik groups in different degrees and retained minor genetic imprint of European-specific lineages, therefore, hinting the existence of multi-ethnic integration events in shaping the genetic landscape of Chinese Hui group.

Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus angularis (Rotifera, Brachionidae)

The two complete mitochondrial genomes were sequenced from the freshwater monogonont rotifer Brachionus angularis. The mitochondrial genome sequences were 10,764 bp (mitochondrial DNA I) and 12,238 bp (mitochondrial DNA II) in size, respectively. The gene structure and its orientation of 12 protein-coding genes (PCGs) of complete mitochondrial genomes of B. angularis was identical to those shown in other marine rotifers and the freshwater rotifer Brachionus rubens, but was different from the freshwater rotifer Brachionus calyciflorus. Of 12 PCGs, one gene (ND5) had incomplete stop codon. Furthermore, the start codon for CO1, ND4L, ND5, and CO2 was GTG, while the start codon for ND3 and other PCGs was ATA and ATG, respectively. The base composition of 12 PCGs in B. angularis mitogenome showed 20.4% for A, 47.3% for T, 17.5% for C, and 14.8% for G, respectively. The mitochondrial genome A + T base composition (67.7%) of 12 PCGs was higher than G + C (32.3%), while the complete mitochondrial genome A + T base composition (66.3%) was higher than G + C (33.7%).

The complete mitochondrial genome analysis and phylogenetic position of the short barbeled grunter Hapalogenys nigripinnis (Lobotiformes: Hapalogenyidae) from Jeju island, Korea

This study analyzed the complete mitochondrial genome of the short barbeled grunter Hapalogenys nigripinnis (Accession number: MT374064). The complete mitogenome was 16,476 bp long and included 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. Nucleotide composition of the genome was A: 28.70%, T:27.46%, G: 15.73%, and C: 28.11%. All genes were encoded on the H-strand, except for the NADH dehydrogenase subunit (ND6) and 8 tRNA genes. When compared this sequence with the mitogenome of Chinese black grunt, Korean short barbeled grunter showed difference of 64 bp of nucleotide sequence in 20 genes. Phylogenetic tree was constructed using the neighbor-joining (NJ) method and showed the phylogenetic position of the short barbeled grunter in Korea.

The complete mitochondrial genome of Carpodacus pulcherrimus (Passeriformes: Fringillidae)

The Himalayan Beautiful Rosefinch Carpodacus pulcherrimus, belongs to the family Fringillidae, distributed in central Himalayas from India (Himachal Pradesh) to southwest China and Bhutan. The conservation status of this species is least concern (LC) in IUCN. In this study, the complete mitogenome of C. pulcherrimus was determined. The mitogenome is a circular molecule of 16,797 bp in length, containing 13 protein-coding genes, 2 ribosome RNA genes, 22 transfer RNA genes, and 1 non-coding region. We reconstructed a phylogenetic tree based on Bayesian inference for other 14 Fringillidae species. The new mitogenome data would provide useful information for application in conservation genetics and further clarify phylogenetic evolution of this species.

Characterization of the mitochondrion genome of a Chlorella vulgaris strain isolated from rubber processing wastewater

Chlorella vulgaris ITBBA3-12 was isolated from the rubber processing wastewater and has a role in wastewater purification. Its complete mitogenome contains 88754 bp, with a G + C content of 29.7%. A total of 64 genes were annotated, including 34 protein-coding genes, 27 tRNA genes, three rRNA (rrn23, rrn16, and rrn5). Phylogenetic analysis using the mitogenomes of Trebouxiophyceae species indicated that the strain ITBBA3-12 is closely related to C. vulgaris strain UTEX259 and NJ-7, and they clustered in the Chlorella lineage.

The complete mitochondrial genome of the freshwater crab Neilupotamon xinganense (Decapoda: Brachyura: Potamoidea)

In this study, we first obtained the complete mitochondrial genome of Neilupotamon xinganense (Decapoda: Brachyura: Potamoidea). The genome is 16,965 bp in length and typically consists of 37 genes (13 protein-coding genes, 22 tRNAs genes, two rRNAs genes, and one putative control region). In addition, the mitogenome has 20 non-coding regions ranging from 1 to 683 bp in length. This study provides DNA data for further researches on population genetics and phylogenetics.

Complete mitochondrial genome of the water vole, Microtus richardsoni (Cricetidae, Rodentia)

Water voles (Microtus richardsoni) are sensitive species distributed in the mountains of Canada (Alberta, British Columbia), and the United States of America (Idaho, Montana, Oregon, Utah, Washington, and Wyoming). We assembled the complete circular M. richardsoni mitogenome, which is 16,285 bp in length and encodes 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. We estimated the phylogenetic tree of M. richardsoni and 24 related arvicoline species with two outgroup species: Phodopus roborovskii and Cricetus cricetus.

The complete mitochondrial genome of the freshwater crab Chinapotamon maolanense (Decapoda: Brachyura: Potamoidea)

The complete mitochondrial genome of Chinapotamon maolanense was obtained for the first time. The complete mitochondrial genome of C. maolanense is 17,130 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. In addition, the mitogenome has 18 noncoding regions ranging from 1 to 1553 bp in length.

Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

Shepherd's purse (Capsella bursa-pastoris) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in A. thaliana.

The complete mitochondrial genome of the freshwater crab Potamiscus motuoensis (Decapoda: Brachyura: Potamoidea)

Potamiscus motuoensis is the only one freshwater crab species distributed in Yarlung Zangbo River Grand Canyon and its complete mitochondrial genome was obtained for the first time. The complete mitochondrial genome of P. motuoensis is 17,971 bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. In addition, the mitogenome has 19 noncoding regions ranging from 1 to 1396 bp in length. The report of the mitochondrial genome will enrich the species diversity of Yarlung Zangbo River Grand Canyon and provide data support for further research.

Complete mitochondrial genome of freshwater fish, Microphysogobio jeoni (Actinopterygii, Cypriniformes, Cyprinidae), from South Korea

In this study, we determined the complete mitochondrial genome sequences of cyprinid freshwater fish, Microphysogobio jeoni, belonging to the subfamily Gobioninae in the order Cypriniformes. The complete mitogenome of M. jeoni was 16,602 bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The gene order was identical with other Microphysogobio species. The overall nucleotide composition of M. jeoni was A + T: 56.1% and G + C: 43.9%, with slightly AT bias. In the phylogenetic tree, M. jeoni and other congeneric species clearly formed a monophyletic clade, and each species distinguished against each other well.

Complete mitochondrial genome of Korean endemic species, Iksookimia yongdokensis (Actinopterygii, Cypriniformes, Cobitidae)

Iksookimia yongdokensis (Actinopterygii, Cypriniformes, Cobitidae) is known as endemic freshwater fish species in Korea. The total length of I. yongdokensis mitogenome is 16,640 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and 1 control region (D-loop). The gene arrangement and content were identical with previously recorded mitogenomes of Iksookimia species. Phylogenetic analysis using PCGs and rRNA was examined by maximum likelihood method indicated that genus Iksookimia is taxonomically not stable status according to Iksookimia species and Cobitis species were grouped together.

Complete mitochondrial genome of the euryhaline monogonont rotifer Brachionus paranguensis (Rotifera, Brachionidae)

The two complete mitochondrial genomes were sequenced from the euryhaline monogonont rotifer Brachionus paranguensis. The mitochondrial genome sequences were 11,603 bp and 12,901 bp in size, and the gene order of 12 protein-coding genes (PCGs) were identical to those of the marine rotifer Brachionus plicatilis, but the positions of some tRNAs (e.g. tRNA-Ile, tRNA-Leu[TTA], tRNA-Phe, and tRNA-Leu[CTC]) of mitochondrial DNA I were different between B. paranguensis and B. plicatilis mitochondrial genomes. Of 12 PCGs, four genes (ND1, ATPase 6, ND5, and ND3) had incomplete stop codons. Furthermore, the start codon of ND4, ND5, and CO3 genes was ATT, while the start codon of other PCGs was ATG. The base composition of 12 PCGs in B. paranguensis mitochondrial genomes was 26.6% for A, 43.0% for T, 17.65% for C, and 12.75% for G, respectively.

Complete mitochondrial genome of the jellyfish, Chrysaora pacifica (Goette, 1886) (Cnidaria, Scyphozoa) and the phylogenetic relationship in the related species

The complete mitochondrial genome sequences of giant jellyfish Chrysaora pacifica, a scyphozoan species inhabiting the Bohai Sea water in China, is firstly described and analyzed in this research. The mitogenome is a circular molecule 16,964 bp in length, including 13 protein-coding genes (Cox 1, Cox2, Atp 8, Atp 6, Cox 3, ND2, ND5, ND 6, ND3, ND4L,ND1,ND4, Cob), 2 tRNAs (trnW, trnM), 2 rRNA genes (small subunit RNA and large subunit RNA). The neighbor-joining (NJ) phylogenetic tree in the related species showed that C. pacifica is close to Chrysaora quinquecirrha.

Phylogenetic relationships and characterization of the complete mitochondrial genome of Eriobotrya japonica in southeast of China

Eriobotrya japonica is an evergreen fruit tree originating in southeastern China. Its fruit is juicy with a pleasant taste and considerable medical value. However, there is no complete mitochondrial (cmt) genome resource for this species. This is the first report of the cmt genome of Eriobotrya japonica from southeastern China. The whole cmt genome was 434,980 bp in size with 37.80% GC content. The cmt genome of Eriobotrya japonica contains 41 protein-coding genes, 22 tRNA genes, and 3 rRNA genes. A phylogenetic maximum-likelihood (ML) tree was constructed based on 22 mitochondrial genomes from plant species. Eriobotrya japonica grouped closely with other Rosaceae species, which provides strong support for the traditional classification.

Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus rubens (Rotifera, Brachionidae)

The two complete mitochondrial genomes were sequenced from the freshwater monogonont rotifer Brachionus rubens. The genome sequences were 12,041 bp and 13,793 bp in size, and the gene order and contents were identical to those of the freshwater rotifer B. rubens China, but were different in three tRNA-Arg, tRNA-Ile, and tRNA-Leu between both B. rubens mitochondrial genomes, while B. calyciflorus had peculiar gene order in mitochondrial DNA I. Of 12 protein-coding genes (PCGs), one gene (ND5) had incomplete stop codons. Furthermore, the start codon of ND4 and CO2 gene was ATT, while the start codon of other PCGs was ATG. The base composition of 12 PCGs in B. rubens mitogenome showed 22.5% for A, 46.5% for T, 16.3% for C, and 14.7% for G, respectively.

First report of the complete mitochondrial genome and phylogenetic analysis of Aphrodita australis (Aphroditidae, Annelida)

In this study, the complete mitochondrial genome of the Aphrodita australis was sequenced. The complete mitochondrial genome was circular and 15,288 bp in length, consisted of a typical set of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region. All these genes are in the heavy strand. The non-coding control region is 672 bp in length, and located between tRNA-Ser and tRNA-Leu. The overall nucleotides base composition of the heavy strand is 31.02% for A, 22.76% for C, 12.49% for G, and 33.73% for T, with a slight A + T-rich feature (64.75%). All of the PCGs begin with ATG as their start codon and the cox 3, cytb and nad 3 are terminated with TAA, atp8, nad4, nad 4l, and nad 6 are terminated with TAG, while others are terminated by incomplete codon T. Seen from the phylogenetic tree, A. australis has a more close relationship with Goniada japonica than other species.

Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae

Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.

Complete mitochondrial genome and phylogenetic analysis of the Gray's pipefish Halicampus grayi Kaup 1856

In the present study, the complete mitochondrial genome of H. grayi was determined and annotated. The circular mitogenome is 16,959 bp in length and contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a control region. Most of the PCGs start with ATG, but CO1 begins with a GTG start codon. Phylogenetic analysis revealed that H. grayi was strictly related to network pipefish Corythoichthys flavofasciatus with 100% bootstrap support value. This work provides basic molecular information that would be useful for further investigation on conservation genetics and evolutionary relationships of H. grayi.

Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus calyciflorus (Rotifera, Brachionidae)

The two complete mitochondrial genomes were sequenced from the Netherlands strain of the freshwater monogonont rotifer Brachionus calyciflorus. The mitochondrial genome sequences were 27,698 bp and 9,906 bp in size, respectively. The gene order and contents of the two B. calyciflorus strains were mostly identical to one another, except for the additional identification and translocation of several tRNAs in mitochondrial DNA I and II. Of 13 protein-coding genes (PCGs), three genes (ND1, ND5, and ND3) had incomplete stop codons. Furthermore, the start codon of ND2, CO2, and CO3 and ND4 genes was ATT, GTG, and ATA, respectively, while the start codon of other PCGs was ATG. The base composition of 13 PCGs of B. calyciflorus (the Netherlands strain) mitogenome showed 31.1% for A, 37.6% for T, 16.5% for C, and 14.8% for G, respectively.

The complete mitogenome of Microhyla fissipes (Anura: Microhylidae) and phylogenetic analysis using GenBank data mining

The complete mitogenome of Microhyla fissipes (16,723 bp) was obtained and analysed. It contains the set of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one non-coding regions. Most of the genes in M. fissipes are located on the H-strand, except for the ND6 and eight tRNA genes which are located on the L-strand. The phylogenetic tree shows that M. fissipes is a sister to the clade composed of M. okinavensis and M. mixtura and places Glyphoglossus yunnanensis as the sister lineage to a clade of Microhyla. This new mitogenome of M. fissipes will provide basic data for further molecular evolution studies in this genus.

Complete mitochondrial genome sequence of Aequorea coerulescens

The complete mitochondrial genome sequences of hydromedusa Aequorea coerulescens, a dominant giant jellyfish distributing in the Yellow Sea and northern East China Sea, China, is first reported in this research. Its mitochondrial DNA has 14,804 bp in length with a linear structure, containing 13 protein-coding genes (PCGs), 2rRNA (s-rRNA and l-rRNA), and 2tRNA (trnaW-TGA and tranM-AGT). The A + T content of the whole base composition of the genome is 72.8% (A: 30.15%; C: 12.33%; G: 14.87%; T: 42.64%). ATG, ATA, and ATT are start codons in five (ATP8, ATP6, COX3, NAD6, NAD4l), four (NAD2, NAD5, NAD1, COX1) and two PCGs (NAD3, NAD4), respectively. COB and COX2 began with GTG and CAA as start codon, respectively. TAA and ATA were the stop codon of ATP6 and NAD5 as well as NAD2 and NAD4, respectively. However, other PCGs were terminated with different stop codons. The NJ phylogenetic tree among the related 15 jellyfish species showed that A. coerulescens is close to Hydra spp.

Complete mitochondrial genome and the phylogenetic position of the common cuckoo, Cuculus canorus bakeri (Aves: Cuculiformes)

The complete mitochondrial genome of Common Cuckoo (Cuculus canorus bakeri) is determined in this study and was deposited in Genbank with accession number MN067867. The length of the mitogenome is 17,457 base pairs (bp) including 13 protein-coding genes (PCGs), 22 transfer (t RNA) RNA genes, two ribosomal RNA (r RNA) genes, one control region (CR) and one short pseudo-control region. The structure is similar to mitochondrial genome of other Cuculiforme species. Phylogenetic tree shows that C. canorus bakeri is closely related to C. poliocephalus. The study has provided useful information for further studies on the evolution, genetic diversity, and phylogenetic relationships in Common Cuckoo.

The complete mitochondrial genome of Silba sp. (Diptera: Lonchaeidae)

The mitochondrial genome of Silba sp. was sequenced and annotated as the first representative of family Lonchaeidae. The complete mitochondrial genome of Silba sp. is 16,008 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs, which has a similar gene structure with other published species of Diptera. The nucleotide composition biases toward A and T is 77.2% of the entirety. All PCGs start with ATN codons, except COI and ND1, and end with TAA or incomplete stop codon. Phylogenetic analyses based on 11 Diptera species supported the monophyly of superfamily Tephritoidea.

The complete mitochondrial genome of common redshank (Tringa totanus)

Tringa totanus is declining throughout Europe and performing protection in China. In this study, we sequenced the complete mitochondrial genome using PCR method. It is the first published complete mitochondrial genome of T. tetanus, which is a circular molecule of 16,818 bp, and it contains 13 typical vertebrate protein-coding genes, 22 tRNA, and two rRNA. The phylogenetic tree was constructed to validate the taxonomic status of T. totanus, exhibiting it a closer relationship to T. glareola.

Complete mitochondrial genome sequence of Parumbrosa polylobata

The complete mitochondrial genome sequences of giant jellyfish Parumbrosa polylobata, a scyphozoan species inhabiting the Yellow Sea cold bottom water in China, is firstly described and analyzed in this research. It is 16,809 bp in length with a linear mitochondrial DNA. The base composition of the genome with A + T bias is 69.7%. There are 13 protein-coding genes (PCGs), 2 tRNAs, and 2 rRNAs. Another two special PCGs, ORF360 and ORF147 with telomeres were found at both ends. The neighbor-joining (NJ) phylogenetic tree among the related 13 species showed that P. polylobata is close to Aurelia spp.

The complete mitochondrial genome of the tube-nosed bat Murina cyclotis (Chiroptera: Vespertilionidae) in China

In this study, the complete mitochondrial genome of a male individual of Murina cyclotis from Guangxi province, China, was sequenced and analyzed. The genome is a circular molecule of 16,463 bp length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Most of the genes were encoded on the H-strand, except for 8 tRNA and ND6 genes. Phylogenetic trees of the complete mitochondrial genome were constructed using RAxML. Our result suggests that M. cyclotis is closely related to M. leucogaster from Korea. The complete mitochondrial genome sequence of M. cyclotis will be helpful for future taxonomic and phylogenetic studies on Murina.

The complete mitochondrial genome of a blowfly Calliphora nigribarbis (Vollenhoven, 1863) (Insecta: Diptera: Calliphoridae)

In the present study, the complete mitochondrial genome of a blowfly Calliphora nigribarbis has been sequenced and analyzed. The length of complete the mitochondrial genome is 16,279 bp, with 39.50% A, 13.20% C, 9.30% G, and 38.0% T nucleotide distribution. The complete mitochondrial genome consists of 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs likewise the most metazoan mitochondrial genomes. Furthermore, phylogenetic relationships of C. nigribarbis in the subfamily Calliphorinae investigated. The results suggested that C. vomitoria is the most related species to C. nigribarbis and the genus Calliphora is not monophyletic. This study provides the first complete mitochondrial genome sequence for the species.

Identification of the complete mitochondrial genome of the king penguin Aptenodytes patagonicus (Sphenisciformes: Spheniscidae: Aptenodytes)

The complete mitochondrial genome of the king penguin Aptenodytes patagonicus was firstly determined. The mitogenome is 17,477 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The total nucleotide composition is 31.0% A, 22.2% T, 33.1% C, and 13.8% G, with a total A + T content of 53.2%. The phylogenetic analysis demonstrates a close relationship between A. patagonicus and A. forsteri. These results provide fundamental information for further phylogeny and genetic studies on Aptenodytes genus.

Identification and analysis of the complete mitochondrial genome of Phyllotreta striolata (Coleoptera, Chrysomelidae)

In this study, the complete mitochondrial genome of Phyllotreta striolata (Coleoptera, Chrysomeloidea, Chrysomelidae) was first determined. The complete genome is 15,689 bp in length. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region (A + T-rich region). The gene organization, nucleotide composition, and codon usage are similar to other Chrysomelidae mitogenomes. The overall nucleotide composition was 39.90% A, 35.94% T, 15.27% C, and 8.89% G, respectively. Phylogenetic analysis both highly supported that P. striolata showed a close relationship with P. undulata. The measure of complete mitogenome sequence of P. striolata will provide fundamental data for the phylogenetic and biogeographic studies of the Chrysomeloidea and Coleoptera.

Characterization of the complete mitochondrial genome of Eriocheir leptognathus with phylogenetic analysis

Eriocheir leptognathus is a dominant species in the Yangtze River estuary. In this study, we first determined the complete mitochondrial genome (mitogenome) of E. leptognathus. The mitogenome is 16,143 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region. Initiation codons ATG and ATT were identified in eight and four PCGs, respectively, while stop codons TAA or TAG were found in eleven genes except for two genes which use incomplete stop codon T–. The phylogenetic analysis indicated that three species (E. hepuensis, E.japonica, E. sinensis) and E. leptognathus are very closely related. The complete mitogenome of E. leptognathus can provide population genetics information to further explore the taxonomic status of this species.