The First Three Mitochondrial Genomes for the Characterization of the Genus Egeirotrioza (Hemiptera: Triozidae) and Phylogenetic Implications

Abstract

(1) Background: Mitochondrial genomes are important markers for the study of phylogenetics and systematics. Triozidae includes some primary pests of Populus euphratica. The phylogenetic relationships of this group remain controversial due to the lack of molecular data. (2) Methods: Mitochondria of Egeirotrioza Boselli were sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary rate of Triozidae, combined with the 13 published mitochondrial genomes. (3) Results: The evolutionary rate of protein-coding genes was as follows: ATP8 > ND6 > ND5 > ND2 > ND4 > ND4L > ND1 > ND3 > APT6 > CYTB > COX3 > COX2 > COX1. We reconstructed the phylogenetic relationships of Triozidae based on 16 triozid mitochondrial genomes (thirteen ingroups and three outgroups) using the maximum likelihood (ML) and Bayesian inference (BI) approaches. The phylogenetic analysis of the 16 Triozidae mitochondrial genomes showed that Egeirotrioza was closely related to Leptynoptera. (4) Conclusions: We have identified 13 PCGs, 22 tRNAs, 2 rRNAs, and 1 control region (CR) of all newly sequenced mitochondrial genomes, which were the mitochondrial gene type in animals. The results of this study provide valuable genomic information for the study of psyllid species.

Keywords: Populus euphratica; Psylloidea; mitochondrial genome; phylogenomics.

Figure 1

Populus euphratica leaves covered with galls.

Figure 2

Mitochondrial genome map showing the mitochondrial genome characteristics of representative species within the genus Egeirotrioza. The arrows indicate the direction of gene transcription. Normative abbreviations are used to represent PCGs and rRNAs, and single letter abbreviations are used to represent tRNAs. Red, green, blue, and orange represent PCGs, tRNA, rRNA, and CR, respectively. The GC content of the complete mitochondrial genome is shown in the second circle. The GC-skew of the complete mitochondrial genome is shown in the third circle. The innermost circle shows the length of the complete mitochondrial genome.

Figure 3

Difference in AT contents of protein-coding genes of Egeirotrioza mitochondrial genomes. (A) First codon positions; (B) second codon positions; (C) third codon positions.

Figure 4

Evolution rates of 13 PCGs of Egeirotrioza. Ka refers to non-synonymous nucleotide substitutions, Ks refers to synonymous nucleotide substitutions, and Ka/Ks refers to the selection pressure of each PCG. The abscissa represents the 13 PCGs, and the ordinate represents the Ka/Ks values.

Figure 5

Sliding window analysis of 13 PCGs and 2 rRNAs in the mitochondrial genomes of 3 species of Triozidae. The red line represents the nucleotide diversity (Pi) value (window size = 200 bp, step size = 20 bp).

Figure 6

Relative synonymous codon usage (RSCU) of mitochondrial protein-coding genes of 3 Triozidae species. The X-axis shows different amino acids, and the Y-axis shows the RSCU value (the number of times a certain synonymous codon is used/the average number of times that all codons encoding the amino acid are used).

Figure 7

Heterogeneity analysis for different matrices. Colored squares represent pairwise Aliscore values. Score values range from −1 (indicating fully random similarity, dark blue) to +1 (indicating non-random similarity).

Figure 8

Phylogenetic trees of Egeirotrioza based on the cds_faa matrix with the PMSF model in IQ-TREE. Support values on nodes indicate r SH-aLRT/UFBoot2, respectively.