A near-complete genome reveals the population evolution of the cotton-melon aphid Aphis gossypii

The cotton-melon aphid Aphis gossypii Glover is a severe pest worldwide. Interhaplotype genomic variation can be used as a starting point to analyze the adaptability of Ap. gossypii. In this study, we utilized long-read PacBio HiFi sequencing and HiC scaffolding techniques to assemble a near telomere-to-telomere gap-free genome assembly of Hap4. The assembly had two gaps totaling 321.24 Mb. We characterized five telomeric repetitive regions (GGTTA)_n, including the four found at the 3′ end of the chromosomes, and obtained new structural information about the telomeres. Due to the improved sequencing technology, we also identified more than 55.03 Mb of repetitive DNA in the genome assembly of Hap4, which contributed significantly to the increase in genome size compared to that of Hap1 and Hap3. Most of the additional repetitive DNA content was located on the X chromosome, and the tandem repeat sequence occupied 16.8% of the X chromosome length. The Hap4 assembly showed that the X chromosome exhibited a greater abundance of AT-rich satDNA arrays (11 satDNA arrays longer than 100 kb) than that observed in the autosomes (A1 and A2 harboured 3 and 1 satDNA arrays). We detected presence-absence variations, insertions, and deletions events between Hap1, Hap3, and Hap4 Ap. gossypii, which had significant effects on gene expression. Additionally, we identified a male-specific glyceraldehyde-3-phosphate dehydrogenase of fungal origin in all strains of Ap. gossypii. This comprehensive genome assembly provides valuable insights into the structural characteristics of highly repetitive regions and allows comparative genomic analyses that facilitate our understanding of Ap. gossypii's adaptation and diversification.