The Phylogenetic Implications of the Mitochondrial Genomes of Macropsis notata and Oncopsis nigrofasciata

The mitochondrial genome sequences of eleven leafhopper species of Batracomorphus (Hemiptera: Cicadellidae: Iassinae) reveal new gene rearrangements and phylogenetic implications

Batracomorphus is the most diverse and widely distributed genus of Iassinae. Nevertheless, there has been no systematic analysis of the genome structure and phylogenetic relationships of the genus. To determine the characteristics of the mitogenomes of Batracomorphus species as well as the phylogenetic relationships between them, we sequenced and compared the mitogenomes of 11 representative Batracomorphus species. The results revealed that the mitogenomes of the 11 Batracomorphus species exhibited highly similar gene and nucleotide composition, and codon usage compared with other reported mitogenomes of Iassinae. Of these 11 species, we found that the mitogenomes of four species were rearranged in the region from trnI-trnQ-trnM to trnQ-trnI-trnM, whereas the remaining species presented a typical gene order. The topologies of six phylogenetic trees were in agreement. Eurymelinae consistently formed paraphyletic groups. Ledrinae and Evacanthinae formed sister taxa within the same clade. Similarly, Typhlocybinae and Mileewinae consistently clustered together. All phylogenetic trees supported the monophyly of Iassinae, indicating its evolutionary distinctiveness while also revealing its sister relationship with Coelidiinae. Notably, the nodes for all species of the genus Batracomorphus were well supported and these taxa clustered into a large branch that indicated monophyly. Within this large branch, four Batracomorphus species with a gene rearrangement (trnQ-trnI-trnM) exhibited distinctive clustering, which divided the large branch into three minor branches. These findings expand our understanding of the taxonomy, evolution, genetics, and systematics of the genus Batracomorphus and broader Iassinae groups.

Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications

Macropsini is a tribe of Eurymelinae in the family Cicadellidae that is widely distributed worldwide. Still, its taxonomic status has been unstable, and the classification of certain clades at the genus level has been controversial. The aim of this study is to address the patterns and processes that explain the structure and the evolution of the mitogenomes of Macropsini, while contributing to the resolution of systematic issues involving five of their genera. To this task, the mitogenomes of 26 species of the tribe were sequenced and characterized, and their phylogenetic relationships were reconstructed. The results revealed that the nucleotide composition of mitochondrial genes in these 26 species was significantly skewed toward A and T. Codons ending with T or A in relative synonymous codon usage were significantly more prevalent than those ending with C or G. The parity plot, neutrality plot, and correspondence analysis revealed that mutation and selective pressure affect codon usage patterns. In the phylogenetic relationships of the Macropsini, the monophyly of Pedionis and Macropsis was well-supported. Meanwhile, Oncopsis revealed paraphyletic regarding Pediopsoides. In conclusion, this research not only contributes the valuable data to the understanding of the mitogenome of the Macropsini but also provides a reference for future investigations on codon usage patterns, potential adaptive evolution, and the phylogeny of the mitogenome within the subfamily Eurymelinae.

The complete mitochondrial genome of Anidiocerus bimaculatus Zhang, Li & Qi, 2008 (Hemiptera: Cicadellidae: Eurymelinae: Idiocerini)

In this study, the complete mitochondrial genome of Anidiocerus bimaculatus was sequenced and annotated for the first time, which belongs to the subfamily Eurymelinae. The mitogenome of A. bimaculatus was 15,267 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region. In this mitogenome, all the PCGs are initially encoded by ATT, ATA, ATG, or TTG, and terminated by TAA, or single T. The overall base composition of A. bimaculatus is 43.6% adenines, 36.0% thymines, 9.1% guanines, and 11.3% cytosines. ML phylogenetic analyses confirmed that Idiocerini forms a monophyletic clade and the newly sequenced A. bimaculatus clustered within the Idiocerini clade based on 13 protein-coding genes and two rRNA genes.

Complete mitogenome and phylogenetic analysis of Hyalinocerus flavoscutatus Cai and Shen 1998 (Hemiptera: Eurymelinae: Idiocerini)

This study presents the initial sequencing and characterization of the complete mitochondrial genome (mitogenome) of Hyalinocerus flavoscutatus, making the first comprehensive exploration of the mitogenome in the Hyalinocerus. Utilizing next-generation sequencing techniques, we identified a circular DNA molecule spanning 15,307 bp. The mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a primary non-coding region. Maximum likelihood phylogenetic evaluation, based on 13 protein-coding genes and two ribosomal RNA genes, robustly supports H. flavoscutatus as the basal group within Idiocerini. This research unveils valuable insights into the mitogenome of H. flavoscutatus and enhances our understanding of phylogenetic placement within the broader context of related tribes.

Two new species of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) from southern China based on morphology and complete mitogenomes

Erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) are utilized to resolve the relationship between the four erythroneurine leafhopper (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini): Arboridia (Arboridia) rongchangensis sp. nov., Thaia (Thaia) jiulongensis sp. nov., Mitjaevia bifurcata Luo, Song & Song, 2021 and Mitjaevia diana Luo, Song & Song, 2021, the two new species are described and illustrated. The mitochondrial gene sequences of these four species were determined to update the mitochondrial genome database of Erythroneurini. The mitochondrial genomes of four species shared high parallelism in nucleotide composition, base composition and gene order, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and an AT control region, which was consistent with majority of species in Cicadellidae; all genes revealed common trait of a positive AT skew and negative GC skew. The mitogenomes of four species were ultra-conservative in structure, and which isanalogous to that of others in size and A + T content. Phylogenetic trees based on the mitogenome data of these species and another 24 species were built employing the maximum likelihood and Bayesian inference methods. The results indicated that the four species belong to the tribe Erythroneurini, M. diana is the sister-group relationship of M. protuberanta + M. bifurcata. The two species Arboridia (Arboridia) rongchangensis sp. nov. and Thaia (Thaia) jiulongensis sp. nov. also have a relatively close genetic relationship with the genus Mitjaevia.

Phylogenomics of endemic Australian Ulopinae (Hemiptera: Cicadomorpha: Cicadellidae)

Ulopinae is a distinctive subfamily of leafhoppers that is widely distributed across the Afrotropical, Palearctic, Indomalayan and Australasian regions. The ulopine fauna of Australia is entirely endemic and includes two tribes of striking appearance, the Ulopini and Cephalelini. Knowledge of these groups is fragmentary and in many instances, no information is available beyond original descriptions. We assess the monophyly, phylogenetic placement and species-level diversity of the Ulopini genus Austrolopa . Phylogenetic analyses based on sequence data from target nuclear loci (18S , 28S , H2A and H3 ) and mitochondrial genomes (15 genes) for 23 membracoid taxa yielded congruent topologies. Our results provide strong evidence for the monophyly of Ulopinae and a clade consisting of Ulopini + Cephalelini. However, a non-monophyletic Cephalelini arises from within a polyphyletic Ulopini. Austrolopa was strongly recovered as monophyletic in all analyses, a result also supported by morphological features. The genus currently includes six species, three of which are described based on morphological and molecular data: Austrolopa botanica , sp. nov. , Austrolopa rotunda , sp. nov. and Austrolopa sublima , sp. nov. A lectotype designation is provided for Austrolopa kingensis Evans, 1937, sp. reval. Our findings illustrate that the Australian Ulopinae is far more diverse than currently circumscribed and several species of Austrolopa are yet to be recognised. ZooBank: urn:lsid:zoobank.org:pub:1480285B-8F61-4659-A929-2B1EF3168868.

Comparative mitochondrial genome analysis of three leafhopper species of the genus Abrus Dai & Zhang (Hemiptera: Cicadellidae: Deltocephalinae) from China with phylogenetic implication

BACKGROUND

The phylogenetic position and classification of Athysanini are poorly defined, as it includes a large group of polyphyletic genera that have historically been assigned to it mainly because they still exhibit the most typical deltocephaline genitalic and external body characters but lack the distinctive characteristics that other tribes possess. The bamboo-feeding leafhopper genus Abrus belong to the tribe Athysanini of subfamily Deltocephalinae, which currently comprises 19 valid described species, and are limited to the Oriental and Palaearctic regions in China. Although the taxonomy of Abrus are well updated, the references on comparative mitogenomic analyses of Abrus species are only known for a single species. In this study, we sequenced and analyzed the complete mitochondrial genomes (mitogenomes) of Abrus daozhenensis Chen, Yang & Li, 2012 (16,391bp) and A. yunshanensis Chen, Yang & Li, 2012 (15,768bp) (Athysanini), and compared with published mitogenome sequence of A. expansivus Xing & Li, 2014 (15,904bp).

RESULTS

These Abrus species shared highly conserved mitogenomes with similar gene order to that of the putative ancestral insect with 37 typical genes and a non-coding A + T-rich region. The nucleotide composition of these genomes is highly biased toward A + T nucleotides (76.2%, 76.3%, and 74.7%), AT-skews (0.091 to 0.095, and 0.095), negative GC-skews (- 0.138, - 0.161, and - 0.138), and codon usage. All 22 tRNA genes had typical cloverleaf secondary structures, except for trnS1 (AGN) which lacks the dihydrouridine arm, and distinctively trnG in the mitogenome of A. expansivus lacks the TψC arm. Phylogenetic analyses based on 13 PCGs, 2 rRNA genes, and 22 tRNA genes consistently recovered the monophyletic Opsiini, Penthimiini, Selenocephalini, Scaphoideini, and Athysanini (except Watanabella graminea, previously sequenced species as Chlorotettix nigromaculatus) based on limited available mitogenome sequence data of 37 species.

CONCLUSION

At present, Abrus belongs to the tribe Athysanini based on both morphological and molecular datasets, which is strongly supported in present phylogenetic analyses in both BI and ML methods using the six concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Phylogenetic trees reconstructed herein based on the BI and ML analyses consistently recovered monophylitic Athysanini, except Watanabella graminea (Athysanini) in Opsiini with high support values.

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)

Japanagallia is a genus of Cicadomorpha in the family of leafhoppers that are plant piercing-sucking insects, and it is difficult to distinguish by morphological characteristics. So far, only one complete mitochondrial genome data has been reported for the genus Japanagallia. Therefore, in order to better understand this group, we assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. Nucleotide composition analysis showed that AT content was higher than GC content, and the protein-coding sequences preferred to end with A/T at the third codon position. Relative synonymous codon usage analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed the codon usage bias of mitochondrial genes was influenced by both natural selection and mutation pressure. In the neutrality plot, the slopes of regression lines were < 0.5, suggesting that natural selection was playing a major role while mutation pressure was of minor importance. The effective number of codons showed that the codon usage bias between genes and genomes was low. Correspondence analysis revealed that the codon usage pattern differed among 13 protein-coding genes. Phylogenetic analyses based on three datasets using two methods (maximum likelihood and Bayesian inference), restored the Megophthalminae monophyly with high support values (bootstrap support values (BS) = 100, Bayesian posterior probability (PP) = 1). In the obtained topology, the seven Japanagallia species were clustered into a monophyletic group and formed a sister group with Durgade. In conclusion, our study can provide a reference for the future research on organism evolution, identification and phylogeny relationships of Japanagallia species.

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.

Structural Characteristics and Phylogenetic Analysis of the Mitochondrial Genomes of Four Krisna Species (Hemiptera: Cicadellidae: Iassinae)

Krisna species are insects that have piercing-sucking mouthparts and belong to the Krisnini tribe in the Iassinae subfamily of leafhoppers in the Cicadellidae family. In this study, we sequenced and compared the mitochondrial genomes (mitogenomes) of four Krisna species. The results showed that all four mitogenomes were composed of cyclic double-stranded molecules and contained 13 protein-coding genes (PCGs) and 22 and 2 genes coding for tRNAs and rRNAs, respectively. Those mitogenomes exhibited similar base composition, gene size, and codon usage patterns for the protein-coding genes. The analysis of the nonsynonymous substitution rate (Ka)/synonymous substitution rate (Ks) showed that evolution occurred the fastest in ND4 and the slowest in COI. 13 PCGs that underwent purification selection were suitable for studying phylogenetic relationships within Krisna. ND2, ND6, and ATP6 had highly variable nucleotide diversity, whereas COI and ND1 exhibited the lowest diversity. Genes or gene regions with high nucleotide diversity can provide potential marker candidates for population genetics and species delimitation in Krisna. Analyses of parity and neutral plots showed that both natural selection and mutation pressure affected the codon usage bias. In the phylogenetic analysis, all subfamilies were restored to a monophyletic group; the Krisnini tribe is monophyletic, and the Krisna genus is paraphyletic. Our study provides novel insights into the significance of the background nucleotide composition and codon usage patterns in the CDSs of the 13 mitochondrial PCGs of the Krisna genome, which could enable the identification of a different gene organization and may be used for accurate phylogenetic analysis of Krisna species.

Description of the whole mitochondrial genome of Bhatia longiradiata (Hemiptera, Cicadellidae, Deltocephalinae: Drabescini) and phylogenetic relationship

BACKGROUND

Mitochondrial genomes are extremely conserved in genetic processes and valuable molecular indications for phylogenetic and evolutionary examination, but the mitochondrial genome of Bhatia has not yet been reported.

OBJECTIVE

The target of this writing was to clarify the structural module of the mitochondrial genes of Bhatia longiradiata, verify the monophyletic of Drabescini, and explore the phylogenetic relationship between Drabescini with other leafhoppers.

METHODS

We performed sequencing and explanatory note of the mitochondrion of Bhatia longiradiata. The phylogeny relation was created by ML and Bayesian approaches using three dissimilar datasets (PCG12, PCG12rRNA, and AA), which were constructed to discuss the phylogenetic status of Bhatia longiradiata.

RESULTS

To report the architectural feature of the chondriosome of Bhatia longiradiata is a seal double-stranded annular molecule with 16,122 bp measurement and cover typically 37 genes. Several tandem repetitive units were observed in an AT enrichment area. The analysis showed that the branching relationships among the six trees were generally consistent, and each of the subfamilies was individually clustered into a monophyletic group within Cicadellidae. Bhatia longiradiata and other members of the Drabescini were aggregated into a clade that was situated within the Deltocephalinae.

CONCLUSION

The mitochondrial genome of Bhatia longiradiata covers 37 typical genes and a control region, which covers six tandem repeats. All species of Drabescini procedure a clade within Deltocephalinae. Drabescini and Scaphoideini form a branch and show a sister relationship with strong support. Therefore, we support the relegation of Selenocephalinae to a clan within Deltocephalinae.

Comparison of mitogenomes of three Petalocephala species (Hemiptera: Cicadellidae: Ledrinae) and their phylogenetic analysis

Ledrinae is a unique group of leafhoppers with a distinct appearance. Petalocephala is the largest Ledrinae genus that is difficult to identify except by dissecting the male genitals. To date, research on Ledrinae is relatively less compared with other leafhoppers. Therefore, to better understand this group, we sequenced and analyzed three complete Petalocephala mitochondrial genomes. We comparatively analyzed these general Petalocephala genomic features (including size, AT content, AT/GC skew, 13 protein-coding gene nucleotide compositions, etc.), and predicted 22 transfer RNA secondary structures. We obtained highly consistent phylogenetic results within Cicadellidae based on mitogenomic data using the maximum likelihood and Bayesian methods. Our results showed that all subfamilies were monophyletic and had a high node support rate, and there was a sister group relationship between Ledrinae and all other leafhopper groups. Furthermore, treehoppers were found to originate from leafhoppers and showed sister group relationships with Megophthalminae. Within Ledrinae, all phylogenetic trees supporting phylogenetic relationships were as follows: ([P. dicondylica + P. gongshanensis] + [Tituria pyramidata + [Ledra auditura + P. gongshanensis]]) Based on the complete mitogenome phylogenetic analysis and the comparison of morphological characteristics, we propose that Petalocephala is not monophyletic.

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.