The Complete Mitochondrial Genome of Four Hylicinae (Hemiptera: Cicadellidae): Structural Features and Phylogenetic Implications

Mitogenomic Analysis and Phylogenetic Implications for the Deltocephaline Tribe Chiasmini (Hemiptera: Cicadellidae: Deltocephalinae)

The grassland leafhopper tribe Chiasmini (Cicadellidae: Deltocephalinae) presently comprises 324 described species worldwide, with the highest species diversity occurring in the Nearctic region but a greater diversity of genera occurring in the Old World. In China, this tribe comprises 39 described species in 11 genera, but the fauna remains understudied. The complete mitogenomes of three species of this tribe have been sequenced previously. In order to better understand the phylogenetic position of Chiasmini within the subfamily Deltocephalinae and to investigate relationships among Chiasmini genera and species, we sequenced and analyzed the complete mitogenomes of 13 species belonging to seven genera from China. Comparison of the newly sequenced mitogenomes reveals a closed circular double-stranded structure containing 37 genes with a total length of 14,805 to 16,269 bp and a variable number of non-coding A + T-rich regions. The gene size, gene order, gene arrangement, base composition, codon usage, and secondary structure of tRNAs of the newly sequenced mitogenomes of these 13 species are highly conserved in Chiasmini. The ATN codon is commonly used as the start codon in protein-coding genes (PCGs), except for ND5 in Doratura sp. and ATP6 in Nephotettix nigropictus, which use the rare GTG start codon. Most protein-coding genes have TAA or TAG as the stop codon, but some genes have an incomplete T stop codon. Except for the tRNA for serine (trnS1(AGN)), the secondary structure of the other 21 tRNAs is a typical cloverleaf structure. In addition to the primary type of G-U mismatch, five other types of tRNA mismatches were observed: A-A, A-C, A-G, U-C, and U-U. Chiasmini mitochondrial genomes exhibit gene overlaps with three relatively stable regions: the overlapping sequence between trnW and trnC is AAGTCTTA, the overlapping sequence between ATP8 and ATP6 is generally ATGATTA, and the overlapping sequence between ND4 and ND4L is generally TTATCAT. The largest non-coding region is the control region, which exhibits significant length and compositional variation among species. Some Chiasmini have tandem repeat structures within their control regions. Unlike some other deltocephaline leafhoppers, the sequenced Chiasmini lack mitochondrial gene rearrangements. Phylogenetic analyses of different combinations of protein-coding and ribosomal genes using maximum likelihood and Bayesian methods under different models, using either amino acid or nucleotide sequences, are generally consistent and also agree with results of prior analyses of nuclear and partial mitochondrial gene sequence data, indicating that complete mitochondrial genomes are phylogenetically informative at different levels of divergence within Chiasmini and among leafhoppers in general. Apart from Athysanini and Opsiini, most of the deltocephaline tribes are recovered as monophyletic. The results of ML and BI analyses show that Chiasmini is a monophyletic group with seven monophyletic genera arranged as follows: ((Zahniserius + (Gurawa + (Doratura + Aconurella))) + (Leofa + (Exitianus + Nephotettix))).

Phylogenetic Analysis of Two New Mitochondrial Genomes of Singapora shinshana and Seriana bacilla from the Karst Region of Southwest China

Leafhoppers have been identified as a serious threat to different plants. To explore the characteristics of mitogenomes and reveal the phylogenetic positions of two species in the Typhlocybinae, complete mitogenomes of Singapora shinshana and Seriana bacilla were sequenced and annotated for the first time with lengths of 15,402 bp and 15,383 bp, respectively. The two mitogenomes contained 13 PCGs, 22 tRNA genes and 2 rRNA genes. The genome content, gene order, nucleotide composition, codon usage and amino acid composition are similar to those of other typical mitogenomes of Typhlocybinae. All 13 PCGs started with ATN codons, except for atp8 (TTA) and nad5 (TTG). All tRNAs were folded into a typical cloverleaf secondary structure, except for tRNA-Ser1 and tRNA-Val. Moreover, phylogenetic trees were constructed and analyzed based on all the PCGs from 42 mitogenomes using maximum likelihood (ML) and Bayesian inference (BI) methods. The results supported that eleven subfamilies are all monophyletic groups, S. shinshana and S. bacilla are members of Erythroneurini, but S. shinshana and the genus Empoascanara have a very close relationship with ((((Empoascanara sipra+ Empoascanara wengangensis) + Empoascanara dwalata) + Empoascanara gracilis) + S. shinshana), and S. bacilla is closely related to the genus Mitjaevia ((Mitjaevia dworakowskae + Mitjaevia shibingensis) + S. bacilla). These results provide valuable information for future study of evolutionary relationships in Typhlocybinae.

Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera)

Helotid beetles are commonly found in places where sap flows from tree trunks and in crevices in bark. The Helotidae family is a rare and primitive group of Cucujoidea. To date, no complete mitochondrial (mt) genome has been sequenced for this family. To better understand the characteristics of the mt genome and the evolution of Cucujoidea, we sequenced and annotated the complete mt genomes of Helota thoracica (Ritsema, 1895) and Helota yehi Lee, 2017 using next-generation sequencing. These are the first record of Helotidae mt genomes. The RNA secondary structures of both species were also predicted in this study. The mt genomes of H. thoracica and H. yehi are circular, with total lengths of 16,112 bp and 16,401 bp, respectively. After comparing the mt genomes of H. thoracica and H. yehi, we observed the gene arrangement, codon usage patterns, base content, and RNA secondary structures of both species to be similar, which has also been noted in other Coleoptera insects. The nucleotide sequence of the coding regions and the control region has small differences. The phylogenetic analysis indicated that Helotidae and Protocucujidae are sister groups and revealed the relationship between seven families; however, the validity of the two series (Erotylid series and Nitidulid series) as larger groups in the superfamily was not supported. The mt phylogenomic relationships have strong statistical support. Therefore, the division of Cucujoidea into series should be re-examined. Our results will provide a better understanding of the mt genome and phylogeny of Helotidae and Cucujoidea and will provide valuable molecular markers for further genetic studies.

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.

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Simple Summary

Mileewinae is a small subfamily of Cicadellidae containing about 160 described species, extensively distributed in the Oriental, Ethiopian and Neotropical regions. Some species are potential pests in agriculture and forestry. The classification of this group has been unstable over the past few decades. Currently, some controversies remain on the monophyly of Mileewinae and phylogenetic relationships of Mileewinae with other subfamilies. To provide further evidence toward answering these questions, two newly completed mitochondrial genomes of Mileewinae species (Mileewa rufivena and Ujna puerana) have been sequenced and analyzed. Results show these two mitochondrial genomes have quite similar structures and features. In phylogenetic analyses, Mileewinae formed a monophyletic group in Cicadellidae in all trees derived from maximum likelihood (ML) and Bayesian inference (BI) methods. In addition, Mileewinae has a closer phylogenetic relationship with Typhlocybinae compared to the Cicadellinae.

Abstract

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications

Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.

Characterization of Two Complete Mitochondrial Genomes of Atkinsoniella (Hemiptera: Cicadellidae: Cicadellinae) and the Phylogenetic Implications

Simple Summary

Atkinsoniella is a large genus of almost 99 species across the world within the subfamily Cicadellinae, which is a large subfamily, comprising more than 2400 species of approximately 330 genera. Some of the Cicadellinae distributed worldwide are known as important agricultural pests. To better understand the mitogenomic characteristics of the genus Atkinsoniella and reveal phylogenetic relationships, the complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced and comparatively analyzed in this study. The mitogenomes of these two Atkinsoniella species were found to be highly conserved, similarly to other Cicadellidae, except for the secondary structure of trnaS1, which formed a loop with the dihydrouridine (DHC) arm. This phenomenon has also been observed in other insect mitogenomes. Phylogenetic analyses, based on mitogenomes using both the maximum likelihood (ML) and Bayesian inference (BI) methods of three datasets, supported the monophyly of Cicadellinae, as well as the other subfamilies, and produced a well-resolved framework of Cicadellidae and valuable data for the phylogenetic study of Cicadellinae.

Abstract

The complete mitochondrial genomes of Atkinsoniella grahami and Atkinsoniella xanthonota were sequenced. The results showed that the mitogenomes of these two species are 15,621 and 15,895 bp in length, with A+T contents of 78.6% and 78.4%, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (CR). For all PCGs, a standard start ATN codon (ATT, ATG, or ATA) was found at the initiation site, except for ATP8, for which translation is initiated with a TTG codon. All PCGs terminate with a complete TAA or TAG stop codon, except for COX2, which terminates with an incomplete stop codon T. All tRNAs have the typical cloverleaf secondary structure, except for trnS, which has a reduced dihydrouridine arm. Furthermore, these phylogenetic analyses were reconstructed based on 13 PCGs and two rRNA genes of 73 mitochondrial genome sequences, with both the maximum likelihood (ML) and Bayesian inference (BI) methods. The obtained mitogenome sequences in this study will promote research into the classification, population genetics, and evolution of Cicadellinae insects in the future.