Abstract: 【Aim】 This study aims to sequence the complete mitochondrial genomes of representative species of Chaitophorinae, so as to analyze the mitochondrial genome architecture and explore the phylogenetic relationships of Chaitophorinae.【Methods】High-throughput sequencing of five species (Chaitophorus populeti, Chaitophorus populifolii, Chaetosiphella stipae, Periphyllus lyropictus and Sipha flava) from four genera within Chaitophorinae was performed using Illumina platform, mitochondrial genome assembly and annotation were then carried out. Comparative analyses were conducted along with previously reported Chaitophorinae mitochondrial genomes of six species (Periphyllus diacerivorus, Periphyllus koelreuteriae, Chaitophorus saliniger, Chaetosiphella stipae, Periphyllus acerihabitans and Laingia psammae) from four genera in NCBI. Phylogenetic trees were reconstructed for Chaitophorinae and its relatives based on 37 gene sequences of 27 complete mitochondrial genomes using maximum likelihood (ML) approach and Bayesian inference (BI). 【Results】 The mitochondrial genomes of Chaitophorinae are 15 787-17 770 bp in size, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, a non-coding control region, and a non-coding repeat region. No gene rearrangement was observed. The nucleotide composition of the Chaitophorinae mitochondrial genomes displays a strong bias toward A+T. All PCGs initiate with standard ATN codons. cox1 and nad4 terminate with T--, except for cox1 in Periphyllus lyropictus, which terminates with TAA, and other PCGs use TAA or TAG as stop codons. atp8 has undergone positive selection and displays the fastest evolutionary rate, whereas cox1 exhibits the slowest evolutionary rate. Except for trnSAGN, which lost the dihydrouridine (DHU) arm, all tRNA genes can form the typical clover-leaf secondary structures. The control region located between rrnS and trnI varies in length from 606 to 1 710 bp, and some species of Chaitophorinae contain repeat sequences in this region. The repeat region situates between trnE and trnF, ranging from 544 to 1 876 bp in length and is composed of species-specific repeat units. The structural composition of the repeat sequences within the control region and the repeat region differs, and the sequence similarity of the repeat units within these two regions is low. Phylogenetic analyses supported the monophyly of Chaitophorinae and its two tribes, Siphini and Chaitophorini. Within Siphini, Sipha flava was placed at the most basal position of this clade. Within Chaitophorini, the monophyletic Chaitophorus and Periphyllus formed a sister group.【Conclusion】In this study, the complete mitochondrial genomes of representative species of Chaitophorinae were sequenced and analyzed. All examined species have the species-specific repeat region between trnE and trnF, which may be a common feature of the Chaitophorinae mitochondrial genomes. Mitochondrial genomes are effective in resolving the phylogenetic relationships within Chaitophorinae. Our study provides valuable molecular data resources for a better understanding of the characteristics of Chaitophorinae mitochondrial genomes, as well as the phylogenetic relationships and evolutionary history of this group.

Key words: Aphids, Chaitophorinae, mitochondrial genome, evolutionary rate, control region, repeat region, phylogenetic relationship