Structural features and phylogenetic implications of Cicadellidae subfamily and two new mitogenomes leafhoppers

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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Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae)

To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species of the subfamily were sequenced and assembled. These were added to the mitogenomes of the eight other species that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) to 15,986 bp in Multinervis guangxiensis (Li and Li, 2013), they all contained 37 genes, and gene order was similar to that in other leafhoppers. Nucleotide composition analysis showed that the AT content was higher than that of GC, and the protein-coding genes usually ended with A/T at the 3rd codon position. The Ka/Ks ratio showed that the CYTB gene has the slowest evolutionary rate, while ND4 is the gene with the fastest evolutionary rate. Relative synonymous codon usage analysis revealed the most frequently used codon was UUA (L), followed by CGA (R), and the least frequently used codon was CCG (P). Parity plot and neutrality plot analyses showed that the codon usage bias of mitochondrial genes was influenced by natural selection and mutation pressure. However, natural selection plays a major role, while the effect of mutation pressure was small. Effective number of codons values were 40.15-49.17, which represented relatively low codon bias. Phylogenetic analyses based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood and Bayesian inference). In the obtained topology, the Megophthalminae species were clustered into a monophyletic group. In conclusion, our results clarify structural modules of the mitochondrial genes and confirm the monophyly of Megophthalminae within Cicadellidae.

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

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.

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.

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.

Characterization and phylogenetic implications of newly sequenced mitogenomes of Five Mileewa and Processina species from China (Hemiptera: Cicadellidae: Mileewinae)

To accumulate evidence of the phylogeny of Mileewinae and the relationships among Mileewa, Processina, and Ujna genera, we sequenced the complete mitochondrial genomes of four Mileewa spp., namely, Mileewa mira, Mileewa lamellata, Mileewa sharpa, and Mileewa amplimacula. The first complete mitogenome of the genus Processina (P. sexmaculata), established by Yang, Deitz & Li from China and comprising five species, was also sequenced in this study. Annotation showed that the five mitogenomes were 14787 -15436 bp in length, and all harbored 37 typical genes. The AT content of the five mitogenomes ranged from 78.3% to 80.2%, which was similar to that of other sequenced Mileewinae species. For protein-coding genes (PCGs), ATN was the start codon, while atp8 and nad5 genes were initiated with TTG, and a great majority of them used TAA or TAG as stop codons, whereas cox2 and nad1 ended with an incomplete codon T-. All tRNAs had a typical cloverleaf secondary structure, except for trnS1, which had a reduced dihydrouridine arm. We further used 59 Membracoidea species and two outgroups to reconstruct phylogenetic trees based on 13 PCGs under an independent partition model with Bayesian inference and Maximum-likelihood methods. Among these two trees, each of the subfamilies Cicadellinae, Typhlocybinae, and Mileewinae were recovered as a monophyletic group with high support values, suggesting that Typhlocybinae was more ancient than Mileewinae and Cicadellinae. Within the Mileewinae subfamily, all species maintained the same relationships and topologies according to both the BI and ML analyses (PP > 0.8, BS > 83) as follows: (M. sharpa + (U. puerana + ((M. ponta + (M. mira + M. lamellata)) + ((M. albovittata + (M. margheritae + M. amplimacula)) + (M. rufivena + (P. sexmaculata + M. alara)))))), and the monophyly of the genera Processina, Mileewa and Ujna were not supported. This study further enriches the Mileewinae mitogenome database and will contribute to future research on the systematics, evolution, and classification of this group.

Mitogenomic phylogeny of Typhlocybinae (Hemiptera: Cicadellidae) reveals homoplasy in tribal diagnostic morphological traits

The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister-group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov.; but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, that is, Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided.

A multi-gene phylogenetic analysis of the leafhopper subfamily Typhlocybinae (Hemiptera: Cicadellidae) challenges the traditional view of the evolution of wing venation

Genera of the diverse leafhopper subfamily Typhlocybinae have traditionally been classified into tribes primarily based on characters of the wing venation and an intuitive phylogeny of this group was previously proposed based on the hypothetical pattern of wing vein evolution. Some recent authors suggested that wing vein characters are not always reliable but few attempts have been made to examine the status and relationships of typhlocybine tribes using rigorous phylogenetic analyses. Phylogenetic analysis of a dataset comprising DNA sequences from five gene regions (H3, H2A, 28S rDNA D2, 16S rDNA, and COI with a total length of 2413 bps) and 61 species representing six previously recognized tribes of Typhlocybinae provides strong support for the monophyly of the subfamily and five of the previously recognized tribes. Most branches received moderate to strong maximum likelihood bootstrap support. The following intertribal relationships were recovered: (Alebrini + Empoascini) + ((Dikraneurini + Erythroneurini) + Typhlocybini). Maximum likelihood analysis recovered Zyginellini (treated as a separate tribe by some authors) as sister to Typhlocybini with low branch support, but the former tribe was derived from within the latter in Bayesian analysis of the same dataset and relationships within Typhlocybini (sensu lato) were generally poorly resolved in both analyses. The relationship of Typhlocybini to other tribes is also unstable, suggesting that more data are needed to resolve the position of this tribe with confidence. Parts of the phylogeny receiving strong support in both analyses contradict the traditional view that Alebrini, the only tribe retaining an appendix in the forewing, is the earliest diverging lineage and possibly gave rise to the other tribes. Ancestral state reconstructions indicate that characters of the wing venation traditionally used for diagnosing typhlocybine tribes are generally conservative but exhibit some homoplasy and may not, by themselves, be reliable for recognizing monophyletic groups within this subfamily.

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.