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

Abstract

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.

Keywords: Macropsini; codon usage bias; mutation pressure; natural selection; phylogeny.

FIGURE 1

Dorsal and lateral views of Macropsis huangbana Li & Tishechkin.

FIGURE 2

The GC skew versus G + C content (%) and AT skew versus A + T content (%) across the mitochondrial genomes of 26 species. Points are grouped in colors according to content, where each point represents a single species.

FIGURE 3

Sliding window analysis presenting distribution of Pi values across PCGs and rRNAs genes, as evaluated in mitochondrial genomes of 26 species.

FIGURE 4

Heat map of RSCU values estimated for each codon across the mitochondrial PCGs of the 26 target species.

FIGURE 5

The frequency distribution of start codons and stop codons of 13 PCGs in 26 species of the Macropsini.

FIGURE 6

PR2‐plot analysis of the 13 mitochondrial protein‐coding genes, where each point represents one of the 26 evaluated species.

FIGURE 7

Neutrality plot analysis of 13 mitochondrial protein‐coding genes showing the correlation between GC values in the first and second x the third codon positions in the 26 evaluated species.

FIGURE 8

Correspondence analysis presenting the distribution of codons regarding their relative synonymous codon usage values across different protein‐coding genes of the 26 evaluated species.

FIGURE 9

The overall frequency of amino acid usage for 13 mitochondrial protein‐coding genes in 26 species.

FIGURE 10

A phylogenetic tree of Macropsini was constructed using MrBayes v3.2.6 based on amino acid sequences (BI: AA). Species marked with an asterisk indicate those that have been previously published.