The first mitochondrial genome from Scopuridae (Insecta: Plecoptera) reveals structural features and phylogenetic implications

Mitochondrial genomes provide insights into the Euholognatha (Insecta: Plecoptera)

BACKGROUND

Euholognatha is a monophyletic group within stoneflies comprised by a superfamily Nemouroidea and a family Scopuridae. Based on morphological data, the family-level phylogenetic relationships within Euholognatha are widely accepted, but there is still controversy among different molecular studies. To better understand the phylogeny of all six extant euholognathan families, we sequenced and analyzed seven euholognathan mitogenomes.

RESULTS

The sequence heterogeneity analysis observed a low degree of compositional heterogeneity in euholognathan mitogenomes. Meanwhile, leuctrid mitogenomes were more heterogeneous than other euholognathan families, which may affect the phylogenetic reconstruction. Phylogenetic analyses with various datasets generated three topologies. The Leuctridae was recovered as the earliest branching lineage, and the sister relationship of Capniidae and Taeniopterygidae was supported by most tree topologies and FcLM analyses. When separately excluding sparsely sampled Scopuridae or high heterogeneity leuctrid taxa, phylogenetic analyses under the same methods generated more stable and consistent tree topologies. Finally, based on the results of this study, we reconstructed the relationships within Euholognatha as: Leuctridae + (Scopuridae + ((Taeniopterygidae + Capniidae) + (Nemouridae + Notonemouridae))).

CONCLUSION

Our research shows the potential of data optimizing strategies in reconstructing phylogeny within Euholognatha and provides new insight into the phylogeny of this group.

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.

The mitochondrial genome analysis of a stonefly, Nemoura longicercia Okamoto, 1922 (Plecoptera: Nemouridae)

To better understand the diversity and phylogeny of Nemouridae, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Nemoura longicercia Okamoto, 1922. The entire mitochondrial genome of N. longicercia was 15,728 bp. It contained 37 representative genes (22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and two ribosomal RNA genes (rRNAs)) and a control region. In this genome, 23 genes were found on the heavy strand (H-strand) and 14 genes were on the light strand (L-strand). All PCGs began with the initiation codon ATN. Eleven PCGs stopped with the termination codon TAA or TAG, while COII and ND5 genes stopped with incomplete codon T. Bayesian’s inference (BI) and maximum-likelihood (ML) methods generated the identical tree topology across the PCGR dataset (13 PCGs plus two rRNAs). The monophyly of each subfamily was well-supported. This analysis supported the clade N. longicercia plus N. papilla as sister taxon to the clade N. meniscata plus N. nankinensis.

Comparative analysis of mitochondrial genomes among the family Peltoperlidae (Plecoptera: Systellognatha) and phylogenetic implications

Nowadays, the position of Peltoperlidae in Systellognatha has been resolved based on morphological analyses. However, there are different opinions based on molecular data. To date, only three peltoperlid mitogenomes are available, and more sampling is needed to obtain precise phylogenetic relationships. In this study, we obtained the complete mitogenomes of Cryptoperla kawasawai (15,832 bp) and Peltoperlopsis sagittata (15,756 bp). Our results show that gene content, gene order, DmTTF binding site, nucleotide composition, codon usage, ribonucleic acid (RNA) structure, and structural elements in the control region are highly conserved in peltoperlids. Heatmap analysis of codon usage shows that the AT-rich codons UUA, AUU, UUU, and AUA were commonly used codons in the Peltoperlidae. Evolutionary rate analyses of protein-coding genes reveal that different genes have been subject to different rates of molecular evolution correlated with the GC content. All tRNA genes in peltoperlid mitogenomes have a canonical cloverleaf secondary structure except for trnS1, whose dihydrouridine arm simply forms a loop. The control region of the family has several distinct structural characteristics and has the potential to serve as effective phylogenetic markers. Phylogenetic analyses support the monophyly of Perloidea, but the monophyly of Pteronarcyoidea is still not supported. The Peltoperlidae is placed as the earliest branch within the Systellognatha, and the estimated phylogenetic relationship is: Peltoperlidae + {(Styloperlidae + Pteronarcyidae) + [Perlidae + (Chloroperlidae + Perlodidae)]}. Our results provide new insight into the phylogeny of this group.

Mitochondrial Genome of Strophopteryx fasciata (Plecoptera: Taeniopterygidae), with a Phylogenetic Analysis of Nemouroidea

Taeniopterygidae is a medium-sized family of stoneflies. The phylogeny of Taeniopterygidae was widely accepted based on the morphological analyses. However, there are different opinions based on molecular data. To date, only two taeniopterygid mitochondrial genomes (mitogenomes) were available, and more sampling is needed to obtain precise phylogenetic relationships. In this research, the Strophopteryx fasciata mitogenome was sequenced and analyzed. The complete mitogenome of S. fasciata was 15,527 bp in length and contained 37 genes and a non-coding control region. Among taeniopterygid mitogenomes, the length variation was minimal in protein-coding genes (PCGs), transfer RNA genes (tRNAs) and ribosomal RNA genes (rRNAs), but very different in the control region. Similar to mitogenomes of other taeniopterygid species, the S. fasciata mitogenome was consistently AT biased and displayed positive AT- and negative GC-skews of the whole mitogenome. Most PCGs used ATN as the start codon and TAA/TAG as the stop codon. The stop codons were far less variable than the start codons in taeniopterygid mitogenomes. All Ka/Ks ratios were less than 1, indicating the presence of purifying selection in these genes. The secondary structures of transfer and ribosomal RNA genes of S. fasciata mitogenome are highly conserved with other taeniopterygid species. In the control region of the S. fasciata mitogenome, some essential elements (tandem repeats, stem–loop structures, and poly−N stretch, etc.) were observed. Two phylogenetic trees were inferred from Bayesian inference (BI) and Maximum Likelihood (ML) methods generated the identical topology across the PCGR dataset. The relationships of five families in Nemouroidea were recovered as Leuctridae + ((Capniidae + Taeniopterygidae) + (Nemouridae + Notonemouridae)). These results will help us understand the mitogenome structure of taeniopterygid species and the evolutionary relationship within Plecoptera.

Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis

The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNA^Ser(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))).

Comparative analysis of four complete mitogenomes from hoverfly genus Eristalinus with phylogenetic implications

The genus Eristalinus is widely distributed globally. Four complete mitochondrial genomes (i.e., mitogenomes) of Eristalinus were sequenced and analyzed in this study: Eristalinus viridis (Coquillett, 1898), E. quinquestriatus (Fabricius, 1781), E. tarsalis (Macquart, 1855), and E. sp. Within these four sequenced mitogenomes, most protein-coding genes (ND2, CO1, COX2, COX3, ND3, ND5, ND4, ND4L, ND6, and Cytb) began with a typical ATN (T/C/G/A) start codon and ended with a stop codon TAA or incomplete T, whereas ND1 began with the start codon TTG. ND3 ended with TAG. The secondary tRNA structure was that of a typical cloverleaf, and only the tRNA-Ser1 lacked a DHU arm. Three and five domains appeared in the 12S and 16S rRNA secondary structures, respectively. The phylogenetic relationships among the four Eristalinus species combined with the published mitogenomes of Syrphidae were reconstructed using the maximum likelihood and Bayesian inference methods, which support the monophyly of the subfamily Syrphinae but do not support that of the subfamily Eristalinae. Of note, Eristalini and Syrphini are monophyletic groups. The mitogenomes of E. viridis, E. quinquestriatus, E. sp., and E. tarsalis are useful for determining the phylogenetic relationships and evolution of Syrphidae.

Mitochondrial genome of Arcynopteryx dichroa (McLachlan, 1872) (Plecoptera: Perlodidae) and phylogenetic analysis

To better understand the diversity and phylogeny of Perlodidae, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Arcynopteryx dichroa. This mitogenome was 16,215 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes (rRNAs), and a control region like other plecopteran. The nucleotide composition of A. dichroa mitochondrial genome obviously biases toward A and T. The A + T content of the whole mitochondrial genome, the PCGs, tRNAs, rRNAs, and the control region were: 69.3%, 67.6%, 69.8%, 71.3%, and 78.7%. Phylogenetic relationship based on the concatenated sequences of 13 PCGs and two ribosomal RNAs showed that the family Perlodidae and Chloroperlidae are sister relationship, family Perlidae being the sister group to the clade (Perlodidae + Chloroperlidae). The monophyly of the family Perlodidae is well supported but the subfamily Perlodinae and Isoperlinae are not monophyletic groups.

Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies

The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.

Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

In this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

Characterization of the complete mitochondrial genome of Nemoura meniscata Li & yang (Plecoptera: Nemouridae) from China

We sequenced the third complete mitochondrial genome of Nemoura meniscataby using the high-throughput sequencing method. The mitochondrial genome harbored 37 typical code genes and a control region with 15,895 bp in length was a double-stranded and circular genome. The nucleotide composition is partial to A and T. Seventy-eight nucleotides were dispersed in 10 intergenic spacers and gene overlaps were also found at 13 gene junctions with 48 nucleotides. In phylogenetic trees, the 13 Nemouridae species form a clade diverged from the outgroup clade. The genus Nemoura and Amphinemura were sister groups which is consistent with the previous study.

Structural and phylogenetic implications of the complete mitochondrial genome of Ledra auditura

We sequenced and annotated the first complete mitochondrial genome (mitogenome) of Ledra auditura (Hemiptera: Cicadellidae: Ledrinae) and reconstructed phylogenetic relationships among 47 species (including 2 outgroup species) on the basis of 3 datasets using maximum likelihood (ML) and Bayesian inference (BI) analyses. The complete L. auditura mitogenome (length, 16,094 bp) comprises 37 genes [13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs], 1 control region, and 2 long non-coding regions. The first long non-coding region (length, 211 bp) is located between tRNA-I and tRNA-Q and the second region (length, 994 bp) between tRNA-S2 and ND1. All PCGs show ATN (Met/Ile) as their start codon and TAR as their stop codon. Except tRNA-S1 (AGN), which lacks the dihydrouridine arm, all tRNAs can fold into the typical cloverleaf secondary structure. The complete L. auditura mitogenome shows a base composition bias of 76.3% A + T (A = 29.9%, T = 46.4%, G = 13.3%, and C = 10.5%), negative AT skew of -0.22, and positive GC skew of 0.12. In ML and BI analyses, L. auditura was clustered with Evacanthus heimianus (Hemiptera: Cicadellidae: Evacanthinae) with strong branch support.

Complete mitochondrial genomes of Bittacus strigosus and Panorpa debilis and genomic comparisons of Mecoptera

Mitochondrial genomes play a significant role in reconstructing phylogenetic relationships and revealing molecular evolution of insects. However, only four mitochondrial genomes were reported in Mecoptera to date. Here, we obtained two new complete mitochondrial genomes of the hangingfly Bittacus strigosus Hagen, 1861 and the scorpionfly Panorpa debilis Westwood, 1846. The results show that the complete mitogenome sequences of B. strigosus and P. debilis are 15,825 and 17,018 bp, respectively, both containing 37 genes and one control region. The mecopteran mitogenomes are highly similar in A + T bias, AT-skew, and GC-skew. Tandem repeats of the control region were discovered in Mecoptera for the first time. The sliding window, genetic distance, and Ka/Ks ratio analyses indicate the purifying selection of 13 protein-coding genes, the lowest evolutionary rate of cox1, and the highest sequence variability of atp8. Considering the sufficiently large size, fast evolution, and high ratio of Ka/Ks, nad4L and nad6 are regarded as potential markers for future phylogenetic analyses, population genetics, and species delimitations in Mecoptera. The phylogenetic relationships were reconstructed for four families of Mecoptera based on all six available mitogenomes using Bayesian inference and maximum likelihood methods. The phylogeny is presented as Boreidae + (Nannochoristidae + (Bittacidae + Panorpidae)).

Comparative mitogenomic analysis of species in the subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved mitochondrial genome organization

The subfamily Amphinemurinae has five genera in China, with each genus of similar morphology. To gain a better understanding of architecture and evolution of mitogenome in Amphinemurinae, mitogenomes of eight species representing four genera (Amphinemura, Indonemoura, Protonemura and Sphaeronemoura) in the subfamily Amphinemurinae were sequenced, and a comparative mitogenomic analysis of five genera (including a published stonefly genus, Mesonemoura) was carried out. By comparative analysis, we found highly conserved genome organization of ten Amphinemurinae species including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. GC content was the most significant factor in determining codon bias among organisms. The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. We also found some important conserved stem and loop in the cloverleaf structure of tRNAs, and found conserved helices and loops in each domain of the secondary structure of rRNAs. The presence of structural elements in the control region is also discussed. The phylogenetic analyses indicated that within Amphinemurinae, Sphaeronemoura was assigned the sister group of Mesonemoura. Our analyses inferred a relationship within Euholognatha: ((Nemouridae + Notonemouridae) + (Taeniopterygidae + Capniidae) + Scopuridae) + Leuctridae.

Mitochondrial genomes of the stoneflies Mesonemourametafiligera and Mesonemouratritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea

In this study, two new mitochondrial genomes (mitogenomes) of Mesonemourametafiligera and Mesonemouratritaenia from the family Nemouridae (Insecta: Plecoptera) were sequenced. The Mesonemourametafiligera mitogenome was a 15,739 bp circular DNA molecule, which was smaller than that of M.tritaenia (15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNA^Ser(AGN) which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.