Mitogenomics: digging deeper with complete mitochondrial genomes

First report of the complete mitochondrial genome of Glyptotendipes pallens (Meigen, 1804) (Diptera: Chironomidae) from Hebei Province, China

Glyptotendipes pallens (Meigen, 1804) serves as a significant bioindicator for monitoring freshwater ecosystems. Despite the performance of COI barcode analyses on G. pallens, the mitogenome of this taxon remains unassembled and unanalyzed. In this study, we provide one newly sequenced complete mitogenome of G. pallens for the first time. The mitogenome is 16,063 bp long with high A + T content, and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a noncoding control region. The phylogenetic analysis strongly supports G. pallens and G. tokunagai as sister species.

The First Complete Mitochondrial Genomes for the Genus Dianema (Siluriformes: Callichthyidae): Dianema longibarbis and D. urostriatum

BACKGROUND/OBJECTIVES

To date, no information is available on the complete mitochondrial genome of the genus Dianema (Siluriformes: Callichthyidae), a callichthyid catfish. In this study, we report on two complete mitochondrial genome sequences of Dianema longibarbis Cope, 1872, and Dianema urostriatum Miranda Ribeiro, 1912, the only two recognized species within the genus Dianema.

METHODS

DNA sequencing was performed using the HiSeq platform to obtain their complete mitogenomes. To confirm phylogenetic distance, two phylogenetic trees were established using maximum-likelihood and Bayesian inference methods with all concatenated protein-coding sequences (PCGs) and two ribosomal RNA (rRNA) genes from the D. longibarbis and D. urostriatum mitogenomes, along with 32 mitogenomes retrieved from Siluriformes.

RESULTS

The complete mitogenomes of D. longibarbis and D. urostriatum are 16,493 and 16,495 base pairs in length, respectively. Their nucleotide compositions are 31.79% A, 27.53% T, 25.86% C, and 14.82% G for D. longibarbis, and 31.69% A, 27.04% T, 26.36% C, and 14.91% G for D. urostriatum. Both mitogenomes contain 13 PCGs, 22 transfer RNA (tRNA) genes, and two rRNA genes. Phylogenetic results based on all PCGs and two rRNAs genes confirm D. longibarbis as a sister species to D. urostriatum in the subfamily Callichthyinae.

CONCLUSIONS

In contrast to the extensive mitochondrial studies on species in the Corydoradinae, species in the Callichthyinae have been largely understudied. This study provides valuable insights into genetic diversity and evolutionary complexity by presenting the first mitochondrial genome analysis of two Dianema species, a genus within the Callichthyinae.

Complete mitochondrial genomes of Sinonovacularivularis and Novaculinachinensis and their phylogenetic relationships within family Pharidae

Pharidae is one of the most ecologically and commercially significant families of marine Bivalvia; however, the taxonomy and phylogeny of Pharidae has been ongoing for quite some time and remains a contentious issue. Here, to resolve some problematical relationships among this family, the complete mitochondrial genomes (mitogenomes) of Sinonovacularivularis (17,159 bp) and Novaculinachinensis (15,957 bp) were assembled, and a comparative mitochondrial genomic analysis was conducted. Both mitogenomes contain 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. Among the published Pharidae mitogenomes, N.chinensis exhibited the smallest genome size but the highest AT content. The results of the phylogenetic trees confirmed the monophyly of the family Solenoidea, and indicated that N.chinensis and Sinonovacula (S.constricta and S.rivularis) were closely related in the family Pharidae. From the CREx analysis, we found that transposition and tandem duplication random losses (TDRLs) might have occurred between Pharidae and Solenidae. Moreover, positive selection was detected in nad5 of the foreground N.chinensis, and divergent evolution occurred at site 144 in the freshwater and marine lineages. Overall, our findings provide new molecular data on the phylogenetic and evolutionary relationships of Pharidae, and contribute to unraveling the salinity adaptations of Pharidae.

The complete mitochondrial genome of medicinally important wood-decaying fungus Tyromyces fissilis within the family Incrustoporiaceae, Polyporales

Tyromyces fissilis (Berk. & M.A.Curtis) Donk 1933, a globally renowned white-rot basidiomycete belonging to the Polyporales order, holds significant potential for lignin degradation, yet its mitochondrial genome has received comparatively little attention. Our study concentrates on a specimen designated T. fissilis NEFU_01, sourced from the Forest Botanical Garden in Heilongjiang Province, China. Utilizing next-generation sequencing (NGS) technology, we have successfully delineated the complete mitochondrial genome of this T. fissilis isolate. The genome is composed of 15 protein-coding genes (PCGs), an array of 24 transfer RNAs (tRNAs), and a pair of ribosomal RNAs (rRNAs), encompassing a total of 163,380 base pairs (bp). Additionally, the genome encodes 28 LAGLIDADG- and 10 GIY-YIG-homing endonucleases. The nucleotide composition is characterized by adenine (A) at 37.02%, cytosine (C) at 12.91%, guanine (G) at 13.04%, and thymine (T) at 37.03%, culminating in a GC content of 25.95%. Subsequently, we undertook a phylogenetic analysis, employing a dataset of 25 mitochondrial genomes to construct a phylogenetic tree. This research represents the first comprehensive foray into understanding the phylogenetic relationships of T. fissilis with its Basidiomycete kin, particularly its sister-group relationship with Phlebia radiata Fr. (1821), thereby laying a substantive groundwork for subsequent evolutionary and taxonomic studies within this mycological cohort.

Description and Phylogenetic Studies on the Complete Mitochondrial Genome of Kingdonella qinghaiensis Zheng (Insecta: Orthoptera: Acrididae)

Kingdonella qinghaiensis Zheng, 1990 a species belonging to the genus Kingdonella Uvarov, 1933, within the family Acrididae in the order Orthoptera, is mainly distributed in Qinghai province, China. In this study, we determined, assembled and annotated the mitochondrial genome of Kingdonella qinghaiensis. The mitogenome is 15,597 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (D-loop). The entire mitogenome exhibits a strong A/T bias, with an A+T content of 75.4%. All 13 PCGs had the typical start codon of ATN (9 ATGs, 2 ATCs and 2 ATTs) and TAA was the most frequent stop codon in Kingdonella qinghaiensis PCGs, except TAGs for ND3 and ND1 genes. A total of 3,730 codons are present in the mitogenomic PCGs of Kingdonella qinghaiensis. Among these, UUA (9.65%) is the most frequent codon for leucine (L), followed by AUU (9.3%) for isoleucine (I), and UUU (8.12%) for phenylalanine (F). The Ka/Ks ratios of the 13 PCGs in Kingdonella qinghaiensis mitogenome ranged from 0.1436 to 0.9107 (0 Collapse

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MESH Headings

• Animals
• Genome, Mitochondrial
• Phylogeny
• Male
• Female
• China
• Grasshoppers/genetics
• Grasshoppers/classification

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Affiliation(s)

Xiaoli Liu College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Yun Fu College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Xinxin Li College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Yuan Li College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Jizhuang Liu College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Yang Hu College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Hong Xueting College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Xunhuan Ding College of Life Science; Huaibei Normal University; Huaibei; 235000; China.
Tao Sun College of Life Science; Huaibei Normal University; Huaibei; 235000; China.

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Phylogenetic Relationship and Characterization of the Complete Mitochondrial Genome of the Cuckoo Species Clamator coromandus (Aves: Cuculidae)

The chestnut-winged cuckoo (Clamator coromandus) is a bird species known for its brood parasitism, laying eggs in the nests of other bird species. However, there is a paucity of genetic information available for this species and their genus Clamator. In this study, we present the first complete mitochondrial genome sequence of C. coromandus and compare it with other species within the Cuculidae family. The mitogenome is a closed circular molecule consisting of 17,082 bp with an organization typical of the mitochondrial genomes of Cuculidae. Alignment of the control regions across Cuculidae species revealed substantial genetic variation and a significant abundance of AT content. A significant difference was detected in AT-skews between brood-parasitic and parental-care species. A distinctive long poly-C sequence was located at the 5' end of domain I. Phylogenetically, C. coromandus is more closely related to Piaya cayana than Ceuthmochares aereus. The phylogenetic analysis indicated a general divergence between species with brood parasitism and those with parental care, with transitions between these behaviors within brood parasitism branches, suggesting multiple evolutionary occurrences of these traits. The complete mitogenome of C. coromandus serves as a valuable resource for further investigation into the taxonomic status and phylogenetic history of Clamator species.

New mitochondrial gene order arrangements and evolutionary implications in the class Octocorallia

The complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date, seven different gene orders (A-G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole class Octocorallia, have been often overlooked. Here, we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from 7 to 14 and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT and GC skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, inverted transpositions and transpositions. Furthermore, gene order rearrangement events were restricted only to some regions of the tree. Overall, different rearrangement events arose independently and from the ancestral and most common gene order, instead of being derived from other rearranged orders. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa.

Complete mitochondrial genome sequence of Nannostomus eques and comparative analysis with Nannostomus beckfordi

The brown pencilfish, Nannostomus eques is a lebiasinid harvested for ornamental purposes; however, its complete mitochondrial genome sequence is still unknown. To enrich the molecular genetic information pertaining to Nannostomus, we present here the first report of the complete mitochondrial genome sequence of Nannostomus eques and compare it with Nannostomus beckfordi. The total lengths of the N. eques and N. beckfordi mitochondrial genomes were 16,673 bp and 16,742 bp, respectively, and there was a double-stranded ring with a heavy chain and a light chain in the whole structures of both. We used PhyloSuite v1.2.1 to construct the maximum likelihood and Bayesian Analysis trees based on tRNAs, rRNAs, and protein-coding genes (PCGs) data and compared them with other Nannostomus species by referring to other studies. Our study found that N. beckfordi has a closer genetic relationship with N. eques than with Lebiasina astrigata, which belongs to the same family, and we discovered some similarities and even rules in Nannostomus species. Our study provides a molecular basis for the conservation and sustainable use of Nannostomus species.

Complete mitochondrial genome of Lepidocephalichthysberdmorei and its phylogenetic status within the family Cobitidae (Cypriniformes)

In this study, the complete mitochondrial genome of Lepidocephalichthysberdmorei was first determined by the primer walking sequence method. The complete mitochondrial genome was 16,574 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop). The gene arrangement pattern was identical to that of other teleosts. The overall base composition was 29.9% A, 28.5% T, 25.5% C, and 16.1% G, with an A+T bias of 58.4%. Furthermore, phylogenetic analyses were conducted based on 13 PCGs from the mitochondrial genomes of 18 cobitid species using with three different methods (Neighbor-joining, Maximum likelihood, and Bayesian inference). All methods consistently showed that the four species of the genus Lepidocephalichthys form a monophyletic group. This study would provide effective molecular information for the Lepidocephalichthys species as well as novel genetic marker for the study of species identification.

The Complete Mitochondrial Genome of Chilo infuscatellus (Lepidoptera: Pyralidae), and Related Phylogenetic Analysis

The Chilo infuscatellus (Lepidoptera: Pyralidae) is a significant pest of sugarcane in China. The genome-level characteristics of this pest are important genetic resources for identification, phylogenetic analysis, and even management. In the present study, the complete mitogenome of C. infuscatellus was sequenced and characterized. The assembled mitochondrial genome is 15,252 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Except for the CGA codon for the cox1 gene, the PCGs are initiated with ATN codons (ATG, ATT, and ATA). These PCGs are terminated with TAA or an incomplete termination codon of a single T. Except for the loss of the "DHU" arm for trnS1, the tRNA genes were folded into the typical cloverleaf structure. The A + T-rich region has a high AT content of 96.19% and contains the motifs "ATAGA" and "ATTTA", as well as a 19 bp poly-T stretch and microsatellite regions. The C. infuscatellus mitogenome exhibits a conserved gene order among lepidopteran insects, with a rearrangement of the trnM gene compared to the ancestral insect gene order. Phylogenetic analysis based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods confirmed the monophyly of Pyralidae and Crambidae within Pyraloidea. The relationships between subfamilies in Pyralidae can be described as (Galleriinae + (Phycitinae + (Pyralinae + Epipaschiinae))). The "PS clade" and "non-PS clade" were formed within the family Crambidae. These findings provide valuable genetic resources for the identification, phylogenetic analysis, and management of sugarcane borers, contributing significantly to our understanding of the phylogeny of Pyraloidea insects and their evolution.

Potential Cryptic Diversity in the Genus Scoliodon (Carcharhiniformes: Carcharhinidae): Insights from Mitochondrial Genome Sequencing

Scoliodon is a genus of small placental sharks living in offshore waters. For a long time, the genus was considered a monotypic genus until a valid species, Scoliodon macrorhynchos, was confirmed in 2010. However, S. muelleri in the same study was not widely recognized because of the lack of evidence. In this study, we obtained the complete mitochondrial genome of the genus Scoliodon from Ranong, Thailand, and tentatively named it Scoliodon sp. By comparing the complete mitochondrial genome with those of two other Scoliodon species and conducting phylogenetic and divergence time analyses, we determined that Scoliodon sp. diverged from the other species. These findings indicate the potential for a new cryptic species (Scoliodon sp.) in the Scoliodon genus. This conclusion was further supported by a subsequent analysis of the published S. laticaudus control region sequences from previous studies. Finally, based on these conclusions, we used machine learning to derive a new identification method for the cryptic species. This approach may be useful for the discovery of new species or cryptic species in other organisms.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

Characterization of the Complete Mitochondrial Genome of the Central Highland Grey-Shanked Douc Langur (Pygathrix cinerea), a Critically Endangered Species Endemic to Vietnam (Mammalia: Primates)

The grey-shanked douc langur (Pygathrix cinerea) is a recently described, critically endangered primate, endemic to Vietnam. In this study, we describe the Central Highland species' complete mitochondrial genome (mitogenome-mtDNA). It is a circular molecule with a length of 16,541 base pairs (bp). The genome consists of 37 genes, consistent with those found in most other vertebrates, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs. A comparison with the mitogenomes of more than 50 primates showed that the mitogenome of Vietnamese Central Highland Pygathrix cinerea has a conservative gene order. We identified 43 nucleotide differences when comparing this genome with a previously published mitogenome of Pygathrix cinerea. It is evident that there are distinct differences between the Pygathrix cinerea we are currently studying and other Pygathrix cinerea specimens. These differences are unlikely to be solely the result of sequencing errors, as the mitogenomes were generated using high-quality methods. The genetic divergence observed between the two Pygathrix cinerea mitogenomes implies the potential existence of at least two distinct lineages or forms of this primate species within its native range in Vietnam.

Exploring the mitochondrial genomes and phylogenetic relationships of trans-Andean Bryconidae species (Actinopterygii: Ostariophysi: Characiformes)

Comparative mitogenomics and its evolutionary relationships within Bryconidae remains largely unexplored. To bridge this gap, this study assembled 15 mitogenomes from 11 Bryconidae species, including five newly sequenced. Salminus mitogenomes, exceeding 17,700 bp, exhibited the largest size, contrasting with a median size of 16,848 bp in the remaining species (Brycon and Chilobrycon). These mitogenomes encode 37 typical mitochondrial genes, including 13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes, and exhibit the conserved gene arrangement found in most fish species. Phylogenetic relationships, based on the maximum-likelihood method, revealed that the trans-Andean species (found in northwestern South America) clustered into two main sister clades. One clade comprised the trans-Andean species from the Pacific slope, Brycon chagrensis and Chilobrycon deuterodon. The other clade grouped the trans-Andean species from the Magdalena-Cauca Basin Brycon moorei and Salminus affinis, with their respective cis-Andean congeners (found in eastern South America), with Brycon rubricauda as its sister clade. Since the current members of Brycon are split in three separated lineages, the systematic classification of Bryconidae requires further examination. This study provides novel insights into mitogenome characteristics and evolutionary pathways within Bryconidae, standing as crucial information for prospective phylogenetic and taxonomic studies, molecular ecology, and provides a valuable resource for environmental DNA applications.

Complete mitochondrial genome of Penicillidia dufourii (Diptera: Hippoboscoidea: Nycteribiidae) and phylogenetic relationship

Penicillidia dufourii (Westwood 1834) is a specialized parasite categorized under family Nycteribiidae that prefers to parasitize the body surface of various bats under the genus Myotis. Many species of the family Nycteribiidae are carriers of various pathogens; however, research on P. dufourii remains scarce, and studies on its molecular identification and population genetic structure are still lacking. In this study, the complete mitochondrial genome of P. dufourii was elucidated for the first time using Illumina sequencing. The mitochondrial genome is 15,354 bp in size and encodes approximately 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Analysis of 13 protein-coding genes revealed that UUA, UCA, CGA, and GGA were the most common codons, while nad4L had the fastest evolutionary rate and cox1 the slowest. Phylogenetic analysis based on the mitochondrial genome indicated that P. dufourii is clustered with other species of the family Nycteribiidae and is most closely related to Nycteribia parvula and Phthiridium szechuanum.

Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda

In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.

Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae)

The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.

Comparative Mitogenomics and Phylogenetic Implications for Nine Species of the Subfamily Meconematinae (Orthoptera: Tettigoniidae)

Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of Xizicus, Xiphidiopsis and Phlugiolopsis was not supported.

Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae)

Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.

Molecular identification and phylogenetic analysis of the mitogenome in endangered giant nuthatch Sitta magna (Passeriformes, Sittidae)

The Giant Nuthatch Sitta magna (family Sittidae) is a passerine bird, the quantification of the number of habitats and species on a global scale remains low. Most species are restricted to low elevations in southwest China, eastern Myanmar, and northern Thailand. To characterize the mitochondrial genome sequence of S. magna and its phylogenetic relationships with other members within the genus Sitta, the mitochondrial genome of S. magna was sequenced using the whole genome shotgun method. The sequencing results showed that the mitochondrial genome was 16,829 bp long and consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (D-loop). All tRNAs were predicted to form a typical clover secondary structure. Among the 13 PCGs, only the start codon in COI was ATC, the start codon by the remaining 12 PCGs was ATG, and the stop codons were TAG, TAA, AGG, AGA, and TA. Bayesian inference and maximum likelihood phylogenetic analysis of the sequences of 17 species generated consistent well-supported phylogenies. The family Polioptilidae and the family Troglodytidae were closely related, and the family Sittidae was confined to a single branch. The genus Sitta in the family Sittidae was mainly clustered into three branches. Our findings provide new mitochondrial genomic data that could be used for phylogenetic and taxonomic studies; our results also certificate into the phylogenetic relationships within the genus Sitta ((S. himalayensi+(S. nagaensis + S. europaea))+(S. villosa + S. yunnanensis))+(S. carolinensis + S. magna).

Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers

In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.

Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis

The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.

The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily

The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.

The complete mitochondrial genome of Chibiraga houshuaii (Lepidoptera, Limacodidae) and its phylogenetic implications

Chibiraga is a mall East Asian genus in the family Limacodidae (slug-moths). The latter includes many agricultural pests. Mitochondrial genome analysis is an important tool for studying insect molecular identification and phylogenetics. However, there are very few mitogenome sequences available for Limacodidae species, and none for the genus Chibiraga at all. To explore the mitogenome features of Chibiraga and verify its phylogenetic position, the complete mitogenome of Chibiraga houshuaii was sequenced and annotated. The complete 15,487 bp genome encoded 37 mitochondrial genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Most of the PCGs had typical ATN start codons and terminated with TAA or a single T residue. UUA (Leu2), AUU (Ile), UUU (Phe), AUA (Met) and AAU (Asn) were the five most frequently used codons. All tRNAs were folded into cloverleaf secondary structure, except for trnS1, which lacked the DHU arm. Phylogenetic analyses within the superfamily Zygaenoidea were performed based on multiple datasets from mitochondrial genes. The results showed that the families Phaudidae, Limacodidae and Zygaenidae were respectively recovered as monophyly; C. houshuaii was clustered in a clade with nettle type larvae in Limacodidae.

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications

Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.

The complete mitochondrial genome of the mauve stinger jellyfish Pelagia noctiluca Forskål, 1775 (Cnidaria, Scyphozoa, Semaeostomeae) with phylogenetic analysis

This study determined the complete mitochondrial genome of the jellyfish Pelagia noctiluca (Scyphozoa, Semaeostomeae) for the first time. The genome was a linear molecule of 16,390 bp in length and 59.3% AT. It comprised of 13 typical protein-coding genes (cox1-3, nd1-6, nd4L, atp6, atp8, and cytB), two ribosomal RNAs (16S and 12S rRNA), and two tRNAs (trnM and trnW). In addition, we detected two additional open reading frames (polB and ORF314) at one end of the genome. The gene-coding structures were identical to those of other scyphozoans. Based on a molecular phylogeny constructed using 13 protein-coding genes, P. noctiluca has the closest genetic relationship with the genus Chrysaora (Semaeostomeae).

How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures?

Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.

Comparative mitogenomic analysis of three bugs of the genus Hygia Uhler, 1861 (Hemiptera, Coreidae) and their phylogenetic position

Hygia Uhler, 1861 is the largest genus in the bug family Coreidae. Even though many species of this genus are economically important, the complete mitogenomes of Hygia species have not yet been reported. Therefore, in the present study, the complete mitogenomes of three Hygia species, H.lativentris (Motschulsky, 1866), H.bidentata Ren, 1987, and H.opaca (Uhler, 1860), are sequenced and characterized, and submitted in a phylogenetic analysis of the Coreidae. The results show that mitogenomes of the three species are highly conserved, typically with 37 genes plus its control region. The lengths are 16,313 bp, 17,023 bp, and 17,022 bp, respectively. Most protein-coding genes (PCGs) in all species start with the standard codon ATN and terminate with one of three stop codons: TAA, TAG, or T. The tRNAs secondary structures of all species have a typical clover structure, except for the trnS1 (AGC) in H.bidentata, which lacks dihydrouridine (DHU) arm that forms a simple loop. Variation in the length of the control region led to differences in mitochondrial genome sizes. The maximum-likelihood (ML) and Bayesian-inference (BI) phylogenetic analyses strongly supported the monophyly of Hygia and its position within Coreidae, and the relationships are ((H.bidentata + (H.opaca + (H.lativentris + Hygia sp.))). The results provide further understanding for future phylogenetic studies of Coreidae.

The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales

The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.

The Complete Mitochondrial Genome of Box Tree Moth Cydalima perspectalis and Insights into Phylogenetics in Pyraloidea

To resolve and reconstruct phylogenetic relationships within Pyraloidea based on molecular data, the mitochondrial genome (mitogenome) was widely applied to understand phylogenetic relations at different taxonomic levels. In this research, a complete mitogenome of Cydalima perspectalis was recorded, and the phylogenetic position of C. perspectalis was inferred based on the sequence in combination with other available sequence data. According to the research, the circular mitochondrial genome is 15,180 bp in length. It contains 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), 13 typical protein-coding genes (PCGs), and a non-coding control region. The arrangement of a gene of the C. perspectalis mitogenome is not the same as the putative ancestral arthropod mitogenome. All of the PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is undertaken by CGA. Five genes have incomplete stop codons that contain only ‘T’. All tRNA genes display a typical clover–leaf structure of mitochondrial tRNA, except for trnS1 (AGN). The control region contained an ‘ATAGG(A)’-like motif followed by a poly-T stretch. Based on the mitochondrial data, phylogenetic analysis within Pyraloidea was carried out using Bayesian inference (BI) and maximum likelihood (ML) analyses. Phylogenetic analysis showed that C. perspectalis is more closely related to Pygospila tyres within Spilomelinae than those of Crambidae and Pyraloidea.

The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea

BACKGROUND

In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed.

OBJECTIVE

The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea.

METHODS

The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks.

RESULTS

This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution.

CONCLUSION

Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.

First Record of Osphya (Melandryidae: Osphyinae) from Chinese Mainland Based on Morphological Evidence and Mitochondrial Genome-Based Phylogeny of Tenebrionoidea

Osphya Illiger (Melandryidae: Osphyinae) as a species-poor insect group, exhibits a widespread distribution in the Northern Hemisphere, however, the research of the genus is poorly documented especially in East Asia. Herein, an interesting species is discovered in Shennongjia National Natural Reserve (Hubei, China). The examination of morphological characters and comparisons with others show it to be a new member of Osphya, which is described under the name of O. sinensis sp. n. The characteristic photos and a key to the species of Osphya from East Asia are provided. Meanwhile, the mitochondrial genome of O. sinensis sp. n. is sequenced and annotated. Based on this obtained mitogenome and the publicly available data, we reconstructed the phylogeny of Tenebrionoidea by different cladistics methods to investigate the relationships between the new species with others. The results consistently recover O. sinensis sp. n. sister to O. bipunctata (Fabricius) with high supporting values, which further confirm the placement of the new species in the genus Osphya. This is the first time reporting the genus Osphya, the only representative genus of melandryid Osphyinae from mainland China, which enriches the diversity of beetles from the Chinese fauna at both generic and subfamilial levels.

The mitochondrial genomes of the Geometroidea (Lepidoptera) and their phylogenetic implications

The Geometroidea is a large superfamily of Lepidoptera in species composition and contains numerous economically important pest species that cause great loss in crop and forest production. However, understanding of mitogenomes remains limited due to relatively fewer mitogenomes previously reported for this megadiverse group. Here, we sequenced and annotated nine mitogenomes for Geometridae and further analyzed the mitogenomic evolution and phylogeny of the whole superfamily. All nine mitogenomes contained 37 mitochondrial genes typical in insects, and gene organization was conserved except for Somatina indicataria. In S. indicataria, the positions of two tRNAs were rearranged. The trnR was located before trnA instead of after trnA typical in Lepidoptera, whereas the trnE was detected rarely on the minority strand (N-strand). This trnR-trnA-trnN-trnS1-trnE-trnF newly recognized in S. indicataria represents the first gene rearrangement reported for Geometroidea and is also unique in Lepidoptera. Besides, nucleotide composition analyses showed little heterogeneity among the four geometrid subfamilies involved herein, and overall, nad6 and atp8 have higher nucleotide diversity and Ka/Ks rate in Geometridae. In addition, the taxonomic assignments of the nine species, historically defined by morphological studies, were confirmed by various phylogenetic analyses based on the hitherto most extensive mitogenomic sampling in Geometroidea.

Characterizing the Complete Mitochondrial Genomes of Three Bugs (Hemiptera: Heteroptera) Harming Bamboo

Herein, we report the mitochondrial genomic characteristics of three insect pests, Notobitus meleagris, Macropes harringtonae, and Homoeocerus bipunctatus, collected from bamboo plants in Guizhou Province, China. For the first time, the damaged conditions and life histories of M. harringtonae and H. bipunctatus are described in detail and digital photographs of all their life stages are provided. Simultaneously, the mitochondrial genome sequences of three bamboo pests were sequenced and analyzed. Idiocerus laurifoliae and Nilaparvata lugens were used as outgroups, and the phylogenetic trees were constructed. The mitochondrial genomes of the three bamboo pests contained 37 classical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNAs (tRNAs), and a control region, with a total length of 16,199 bp, 15,314 bp, and 16,706 bp, respectively. The A+T values of the three bamboo pests were similar, and trnS1 was a cloverleaf structure with missing arms. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML), supported that N. meleagris and H. bipunctatus belonged to the Coreoidea family, whereas M. harringtonae belonged to the Lygaeoidea family with high support values. This study involves the first complete sequencing of the mitochondrial genomes of two bamboo pests. By adding these newly sequenced mitochondrial genome data and detailed descriptions of life histories, the database of bamboo pests is improved. These data also provide information for the development of bamboo pest control methods by quick identification techniques and the use of detailed photographs.

Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda)

Conflicting phylogenetic signals are pervasive across genomes. The potential impact of such systematic biases may be reduced by phylogenetic approaches accommodating for heterogeneity or by the exclusive use of homoplastic sites in the datasets. Here, we present the complete mitogenome of Lynceus grossipedia as the first representative of the suborder Laevicaudata. We employed a phylogenomic approach on the mitogenomic datasets representing all major branchiopod groups to identify the presence of conflicts and concordance across the phylogeny. We found pervasive phylogenetic conflicts at the base of Diplostraca. The homogeneity of the substitution pattern tests and posterior predictive tests revealed a high degree of compositional heterogeneity among branchiopod mitogenomes at both the nucleotide and amino acid levels, which biased the phylogenetic inference. Our results suggest that Laevicaudata as the basal clade of Phyllopoda was most likely an artifact caused by compositional heterogeneity and conflicting phylogenetic signal. We demonstrated that the exclusive use of homoplastic site methods combining the application of site-heterogeneous models produced correct phylogenetic estimates of the higher-level relationships among branchiopods.

The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae)

The complete mitochondrial genome (mitogenome) of the sawfly, Nesodiprion zhejiangensis Zhou & Xiao, was sequenced, assembled, and deposited in GenBank (Accession Number: OM501121). The 15,660 bp N. zhejiangensis mitogenome encodes for 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and an AT-rich region of 450 bp in length. The nucleotide composition is biased toward adenine and thymine (A + T = 81.8%). Each PCG is initiated by an ATN codon, except for cox2, which starts with a TTG. Of 13 PCGs, 9 have a TAA termination codon, while the remainder terminate with a TAG or a single T. All tRNAs have the classic cloverleaf structure, except for the dihydrouridine (DHU) arm of tRNA^val, which forms a simple loop. There are 49 helices belonging to 6 domains in rrnL and 30 helices belonging to 4 domains in rrnS. In comparison to the ancestral architecture, N. zhejiangensis has the most rearranged mitogenome in Symphyta, in which rearrangement events of local inversion and transposition are identified in three gene clusters. Specifically, the main hotspot of gene rearrangement occurred between rrnS and trnY, and rearranged from rrnS-(AT-rich region)-I-Q-M-nd2-W-C-Y to rrnS-Q-W-C-nd2-I-M-(AT-rich region)-Y, involving a local inversion event of a large gene cluster and transposition events of some tRNAs. Transposition of trnA and trnR (rearranged from A-R to R-A) was observed at the nd3-nd5 gene junction while shuffling of trnP and trnT (rearranged from T-P to P-T) occurred at the nd4l-nd6 gene junction. While illegitimate inter-mtDNA recombination might explain the opposite orientations of transcription between rrnS and trnY, transposition events of tRNA in some gene blocks can be accounted for by the tandem duplication/random loss (TDRL) model. Our phylogenetic analysis suggests that N. zhejiangensis is closely related to congeneric species N. biremis and N. japonicus, which together form a sister lineage with the European pine sawfly, Neodiprion sertifer.

Eighteen mitochondrial genomes of Syrphidae (Insecta: Diptera: Brachycera) with a phylogenetic analysis of Muscomorpha

In this study, 18 mitochondrial genomes (mitogenomes) of Syrphidae were sequenced. These mitogenomes ranged from 15,648 to 16,405 bp and contained 37 genes that were similar to those from other Syrphidae species. Most protein-coding genes (PCGs) started with a standard ATN codon and ended with TAA/G. All transfer RNAs (tRNAs) could be folded into the cloverleaf secondary structure except tRNA-Ser (AGN), which lacks a dihydrouridine arm. The secondary structures of ribosomal RNAs (rRNAs) were predicted. Six domains (III is absent in arthropods) and 44 helices were included in the 16S rRNA, and three domains and 24 helices were included in the 12S rRNA. We found three conserved fragments in all syrphid mitogenomes. Phylogenetic analyses were performed based on the nucleotide data of 13 PCGs and two rRNAs from 76 Muscomorpha and three outgroup species. In results the paraphyly of Aschiza and Schizophora were supported, the Acalyptratae was also paraphyletic but the relationships of its superfamilies were difficult to determine, the monophyly of Calyptratea was supported with the relationships of Oestroidea and Muscoidea need to be further reconsidered. Within Syrphidae the monophyly of family level was supported, the Syrphinae were clustered into one branch, while the paraphyly of Eristalinae was still well supported.

Characterization of complete mitochondrial genomes of five noctuoid moths (Lepidoptera: Noctuoidea) and their phylogenetic implications

In this study, the complete mitochondrial genomes of five noctuoid moth species, namely, Paectes cristatrix, Hemichloridia euprepia, Trigonodes hyppasia, Mythimna unipuncta, and Risoba obstructa, were newly sequenced and characterized. Based on our investigations, the five mitogenomes showed sizes of 15409, 15619, 15654, 15403, and 15233 bp, respectively, and encoded 37 genes (13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA genes) and a control region. All protein-coding genes (PCGs) in these mitogenomes had typical ATN start codons except for cox1 and nad1. The non-canonical codon CGA was the starter in H. euprepia and M. unipuncta and TTG was the starter in T. hyppasia for cox1. The unusual codon GTG was the starter in R. obstructa for nad1. All tRNA genes showed distinctive putative cloverleaf structures except trnS1 (AGN), which lacked the dihydrouridine (DHU) stem. Bayesian inference (BI) and maximum likelihood (ML) analyses were employed based on 13 PCGs using 159 taxa among the five families of the superfamily Noctuoidea, and the results showed the monophyly of this superfamily with well-supported values. Phylogenetic analyses showed that the newly sequenced endemic species Hemichloridia euprepia clustered separately along with the subfamilies Cuculliinae and Acronictinae with fairly supported values.

Spatio-Temporal Evolutionary Patterns of the Pieridae Butterflies (Lepidoptera: Papilionoidea) Inferred from Mitogenomic Data

Pieridae is one of the largest and almost cosmopolitan groups of butterflies, which plays an important role in natural ecosystems; however, to date, its phylogeny and evolutionary history have not been fully resolved. In this study, we obtained the complete or nearly complete mitochondrial genomes of 100 pierid taxa (six newly sequenced, sixty extracted from the whole-genome data, and thirty-four directly available from GenBank). At the same time, for the first time, we conducted comparative mitogenomic and phylogenetic analyses based on these mitogenomic data, to further clarify their spatio-temporal evolutionary patterns. Comparative mitogenomic analysis showed that, except for cox2, the GC content of each of the 13 protein-coding genes (PCGs) in the rapidly diverging subfamily Pierinae was higher than in its sister group Coliadinae. Moreover, the dN/dS values of nine genes (atp6, atp8, cox1, cox3, cob, nad1, nad3, nad5, and nad6) in Pierinae were also relatively higher than those in its sister group, Coliadinae. Phylogenetic analysis showed that all the resultant phylogenetic trees were generally in agreement with those of previous studies. The Pierinae family contained six clades in total with the relationship of (Leptosiaini + (((Nepheroniini + Arthocharidini) + Teracolini) + (Pierini + Elodini))). The Pieridae originated in the Palearctic region approximately 72.3 million years ago in the late Cretaceous, and the subfamily Pierinae diverged from this family around 57.9 million years ago in the Oriental region, shortly after the K-Pg mass extinction event; in addition, the spatio-temporal evolutionary patterns of Pierinae were closely correlated with geological events and environmental changes, as well as the host plant coevolutionary scenario in Earth's history. However, some incongruencies were observed between our results and those of previous studies in terms of shallow phylogenies for a few taxa, and should be further investigated.

Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae)

(1) Background: Chironomids are biological indicators, playing an important role in monitoring and assessing the changes in water ecosystems. Mitochondrial genomes have been widely applied as a molecular marker to analyze the taxonomy and phylogeny of insects. However, knowledge of the mitogenomes of Chironomus species is scarce at present, which limits our understanding of the evolutionary relationships among Chironomus. (2) Methods: In our study, the mitogenomes and their basic structure of 12 Chironomus species and one Microchironomus species were newly sequenced. Combined with reported mitogenomes, a total of 15 mitogenomes of Chironomus were selected for a comparative mitogenomic analysis and phylogenetic reconstruction of Chironomus. (3) Results: Each mitogenome of the Chironomus species has the typical 37 genes and a control region. The basic structure of the whole mitogenomes of Chironomus species is relatively conservative, and the genetic arrangements stay the same as the ancestral mitogenome. (4) Conclusions: Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus.

Complete Mitogenome of Oreolalax Omeimontis Reveals Phylogenetic Status and Novel Gene Arrangement of Archaeobatrachia

Species of the genus Oreolalax displayed crucial morphological characteristics of vertebrates transitioning from aquatic to terrestrial habitats; thus, they can be regarded as a representative vertebrate genus for this landing phenomenon. But the present phylogenetic status of Oreolalax omeimontis has been controversial with morphological and molecular approaches, and specific gene rearrangements were discovered in all six published Oreolalax mitogenomes, which are rarely observed in Archaeobatrachia. Therefore, this study determined the complete mitogenome of O. omeimontis with the aim of identifying its precise phylogenetic position and novel gene arrangement in Archaeobatrachia. Phylogenetic analysis with Bayesian inference and maximum likelihood indicates O. omeimontis is a sister group to O. lichuanensis, which is consistent with previous phylogenetic analysis based on morphological characteristics, but contrasts with other studies using multiple gene fragments. Moreover, although the duplication of trnM occurred in all seven Oreolalax species, the translocation of trnQ and trnM occurred differently in O. omeimontis to the other six, and this unique rearrangement would happen after the speciation of O. omeimontis. In general, this study sheds new light on the phylogenetic relationships and gene rearrangements of Archaeobatrachia.

Characterization of four mitochondrial genomes from superfamilies Noctuoidea and Hyblaeoidea with their phylogenetic implications

In the present study, the newly sequenced mitogenomes of three Noctuoid and one Hyblaeoid (Insecta: Lepidoptera) species were annotated based on next-generation sequence data. The complete mitogenome lengths of Oraesia emarginata, Actinotia polyodon, Odontodes seranensis, and Hyblaea puera were 16,668 bp, 15,347 bp, 15,419 bp, and 15,350 bp, respectively. These mitogenomes were found to encode 37 typical mitochondrial genes (13 protein-coding, 22 transfer RNA, 2 ribosomal RNA) and a control region, similar to most Lepidoptera species. Maximum likelihood (ML) methods and Bayesian inference (BI) were used to reconstruct the phylogenetic relationships of the moths. This study showed the relationships of Noctuoid families as follows: (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). Furthermore, the species H. puera was separately clustered from the Noctuoidea member groups. Till now, the species from the superfamily Hyblaeoidea have not been discussed for their phylogenetic relationships. In this study, the complete mitochondrial genome of one species from the superfamily Hyblaeoidea was analysed.

Next-Generation Sequencing of Four Mitochondrial Genomes of Dolichovespula (Hymenoptera: Vespidae) with a Phylogenetic Analysis and Divergence Time Estimation of Vespidae

The wasp genus Dolichovespula (Hymenoptera: Vespidae: Vespinae) is a eusocial wasp group. Due to the taxonomic and phylogenetic issues with the family Vespidae, more genetic data should be gathered to provide efficient approaches for precise molecular identification. For this work, we used next-generation sequencing (also known as high-throughput sequencing) to sequence the mitochondrial genomes (mtgenomes) of four Dolichovespula species, viz. D. flora, D. lama, D. saxonica, and D. xanthicincta 16,064 bp, 16,011 bp, 15,682 bp, and 15,941 bp in length, respectively. The mitochondrial genes of the four species are rearranged. The A + T content of each mtgenome is more than 80%, with a control region (A + T-rich region), 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. There are 7 to 11 more genes on the majority strands than on the minority strands. Using Bayesian inference and Maximum-Likelihood methodologies as well as data from other species available on GenBank, phylogenetic trees and relationship assessments in the genus Dolichovespula and the family Vespidae were generated. The two fossil-based calibration dates were used to estimate the origin of eusociality and the divergence time of clades in the family Vespidae. The divergence times indicate that the latest common ancestor of the family Vespidae appeared around 106 million years ago (Ma). The subfamily Stenogastrinae diverged from other Vespidae at about 99 Ma, the subfamily Eumeninae at around 95 Ma, and the subfamily Polistinae and Vespinae diverged at approximately 42 Ma. The genus Dolichovespula is thought to have originated around 25 Ma. The origin and distribution pattern of the genus Dolichovespula are briefly discussed.

Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtusplautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)

Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtusplautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O.plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioiacunea and calculated the Ka/Ks ratio for each set of PCGs. The highest value of the Ka/Ks ratio within 13 PCGs was found in nad2 with 1.1, suggesting that they were subjected to positive selection. This phenomenon was first discovered in Encyrtidae. Compared with other encyrtid mitogenomes, a translocation of trnW was found in O.plautus, which was the first of its kind to be reported in Encyrtidae. Comparing with ancestral arrangement pattern, wasps reflect extensive gene rearrangements. Although these insects have a high frequency of gene rearrangement, species from the same family and genus tend to have similar gene sequences. As the number of sequenced mitochondrial genomes in Chalcidoidea increases, we summarize some of the rules of gene rearrangement in Chalcidoidea, that is four gene clusters with frequent gene rearrangements. Ten mitogenomes were included to reconstruct the phylogenetic trees of Encyrtidae based on both 13 PCGs (nucleotides of protein coding genes) and AA matrix (amino acids of protein coding genes) using the maximum likelihood and Bayesian inference methods. The phylogenetic tree reconstructed by Bayesian inference based on AA data set showed that Aenasiusarizonensis and Metaphycuseriococci formed a clade representing Tetracneminae. The remaining six species formed a monophyletic clade representing Encyrtinae. In Encyrtinae, Encyrtus forms a monophyletic clade as a sister group to the clade formed by O.plautus and Diaphorencyrtusaligarhensis. Encyrtussasakii and Encyrtusrhodooccisiae were most closely related species in this monophyletic clade. In addition, gene rearrangements can provide a valuable information for molecular phylogenetic reconstruction. These results enhance our understanding of phylogenetic relationships among Encyrtidae.

Description and complete mitochondrial genome of Atkinsoniella zizhongi sp. nov. (Hemiptera: Cicadellidae: Cicadellinae) from China and its phylogenetic implications

A new species, Atkinsoniella zizhongi sp. nov. of the subfamily Cicadellinae, was described and illustrated from China. The new species is similar to A. nigrominiatula (Jacobi, 1944), A. limba Kuoh, 1991, A. dormana Li, 1992, A. peaka Yang, Meng et Li, 2017, and A. divaricata Yang, Meng et Li, 2017. But the characteristics of aedeagus and pygofer process can be used to distinguish them easily. The complete mitochondrial genome of the paratype was sequenced and assembled. The mitogenome of A. zizhongi sp. nov. was 16,483 bp in length, with an A+T content of 75.9%, containing 37 typical genes and a control region (CR). The gene order was consistent with the inferred insect ancestral mitochondrial genome. All of the PCGs were determined to have the typical stop codon TAA or TAG, while COX2 and ND5 ended with incomplete termination codons T and TA, respectively. In addition, phylogenetic trees were reconstructed based on PCGs and rRNAs using both the maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that the intergeneric and interspecific relationships within the subfamily Cicadellinae were completely consistent in all of the phylogenetic trees, except that the different interspecific relationships within the genus Bothrogonia were detected in the ML analysis based on the amino acid sequences. This study enriches the species diversity of Cicadellinae and further promotes research on its phylogeny.

The Nursehound Scyliorhinus stellaris Mitochondrial Genome—Phylogeny, Relationships among Scyliorhinidae and Variability in Waters of the Balearic Islands

The complete mitochondrial DNA sequence of the Nursehound Scyliorhinus stellaris has been determined for the first time and compared with congeneric species. The mitogenome sequence was 16,684 bp in length. The mitogenome is composed of 13 PCGs, 2 rRNAs, 22 transfer RNA genes and non-coding regions. The gene order of the newly sequenced mitogenome is analogous to the organization described in other vertebrate genomes. The typical conservative blocks in the control region were indicated. The phylogenetic analysis revealed a monophyletic origin of the Scyliorhininae subfamily, and within it, two subclades were identified. A significant divergence of Scyliorhinus spp. together with Poroderna patherinum in relation to the group of Cephaloscyllium spp. was observed, except for Scyliorhinus torazame, more related to this last cited clade. A hypothesis of a divergent evolution consequent to a selective pressure in different geographic areas, which lead to a global latitudinal diversity gradient, has been suggested to explain this phylogenetic reconstruction. However, convergent evolution on mitochondrial genes could also involve different species in some areas of the world.