Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

Abstract

Background: Cosmoscartini (Hemiptera: Cercopoidea: Cercopidae) is a large and brightly colored Old World tropical tribe, currently containing over 310 phytophagous species (including some economically important pests of eucalyptus in China) in approximately 17 genera. However, very limited information of Cosmoscartini is available except for some scattered taxonomic studies. Even less is known about its phylogenetic relationship, especially among closely related genera or species. In this study, the detailed comparative genomic and phylogenetic analyses were performed on nine newly sequenced mitochondrial genomes (mitogenomes) of Cosmoscartini, with the purpose of exploring the taxonomic status of the previously defined genus Okiscarta and some closely related species within the genus Cosmoscarta.

Results: Mitogenomes of Cosmoscartini display similar genomic characters in terms of gene arrangement, nucleotide composition, codon usage and overlapping regions. However, there are also many differences in intergenic spacers, mismatches of tRNAs, and the control region. Additionally, the secondary structures of rRNAs within Cercopidae are inferred for the first time. Based on comparative genomic (especially for the substitution pattern of tRNA secondary structure) and phylogenetic analyses, the representative species of Okiscarta uchidae possesses similar structures with other Cosmoscarta species and is placed consistently in Cosmoscarta. Although Cosmoscarta bimacula is difficult to be distinguished from Cosmoscarta bispecularis by traditional morphological methods, evidence from mitogenomes highly support the relationships of (C. bimacula + Cosmoscarta rubroscutellata) + (C. bispecularis + Cosmoscarta sp.).

Conclusions: This study presents mitogenomes of nine Cosmoscartini species and represents the first detailed comparative genomic and phylogenetic analyses within Cercopidae. It is indicated that knowledge of mitogenomes can be effectively used to resolve phylogenetic relationships at low taxonomic levels. Sequencing more mitogenomes at various taxonomic levels will also improve our understanding of mitogenomic evolution and phylogeny in Cercopidae.

Keywords: Cosmoscartini; Mitochondrial genome; Phylogeny; Spittlebug.

Fig. 1

Circular diagram of the nine Cosmoscartini mitogenomes. Different color is performed to show the nucleotide identity of BLAST hits, with the reference genome represented by C. bimacula. The rings are arranged in an order that the most similar genome is placed closest to the outer edge of the circle

Fig. 2

Base composition of various datasets among Cercopidae mitogenomes. (a) Hierarchical clustering of Cercopidae species (y-axis) based on their A + T content; (b) Clustering of species in terms of AT-skew and GC-skew

Fig. 3

Evolutionary rate of each PCG among Cosmoscartini species. Ks, synonymous nucleotide substitutions per synonymous site; Ka, nonsynonymous nucleotide substitutions per nonsynonymous site

Fig. 4

Secondary structures of tRNA families in Cosmoscartini mitogenomes. The nucleotide substitution pattern for each tRNA is modeled using as reference the structure predicted for C. bimacula. Watson-Crick base pairings, GU bonds, and mismatches are illustrated by dashes, solid dots, and hollowed dots, respectively

Fig. 5

Predicted secondary structure of the rrnL in the mitogenome of C. bimacula. Filled circle, nucleotide conserved in nine Cosmoscartini mitogenomes; hollowed circle, nucleotide not conserved. Roman numerals denote the conserved domain structure. Watson-Crick pairs are connected by dashes, whereas GT pairs are joined by dots

Fig. 6

Predicted secondary structure of the rrnS in the mitogenome of C. bimacula. Filled circle, nucleotide conserved in nine Cosmoscartini mitogenomes; hollowed circle, nucleotide not conserved. Roman numerals denote the conserved domain structure. Watson-Crick pairs are connected by dashes, whereas GT pairs are joined by dots

Fig. 7

Phylogenetic tree inferred from mitogenomes of Cosmoscartini. Squares at the nodes are Bayesian posterior probabilities (PP) for 1, 3, 5, and 7, Bootstrap values (BS) for 2, 4, 6, and 8. Dataset of P123, 1 and 2; P12, 3 and 4; P123R, 5 and 6; P12R, 7 and 8. * indicates PP = 1.00 and BS = 100 in all inferences