Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily Aphid Rhopalosiphum nymphaeae (Hemiptera: Aphididae) Mitochondrial Genome

The water lily aphid, , is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of is 15,772 bp in length, with a high A+T c...

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Published in:International journal of molecular sciences 2024-11, Vol.25 (21), p.11336
Main Authors: Shi, Aiyang, Li, Chenyang, Farhan, Muhammad, Xu, Chunhao, Zhang, Yanjin, Qian, Hongye, Zhang, Shuai, Jing, Tianxing
Format: Article
Language:English
Subjects:
Amino acids
Animals
Aphididae
Aphids - classification
Aphids - genetics
Bats
Bias
Codon
Codon - genetics
Codon Usage
Diseases and pests
Evolution, Molecular
Genes
Genetic aspects
Genome, Mitochondrial - genetics
Genomes
Insects
Mitochondrial DNA
Natural history
Phylogenetics
Phylogeny
Physiological aspects
RNA, Transfer - genetics
Selection, Genetic
Transfer RNA
Water lilies
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Summary:The water lily aphid, , is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as , is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms252111336