A comparative genomic analysis at the chromosomal-level reveals evolutionary patterns of aphid chromosomes

• DOI: 10.1038/s42003-025-07851-0
• Publication Date: 2025-03-13T12:38:31Z
• Authors: Chen Huang; Bingru Ji; Zhaohui Shi; Jiangyue Wang; Jiaqing Yuan; Peng Yang; Xiao Xu; Haohao Jing; Lulu Xu; Jing Fu; Le Zhao; Yandong Ren; Kun Guo; Gang Li
• Keywords: Comparative genomic hybridization

Genomic rearrangements are primary drivers of evolution, promoting biodiversity. Aphids, an agricultural pest with high species diversity, exhibit rapid chromosomal evolution and diverse karyotypes. These variations have been attributed to their unique holocentric chromosomes parthenogenesis, though this hypothesis has faced scrutiny. In study, we generated a chromosomal-level reference genome assembly the celery aphid (Semiaphis heraclei) conducted comparative genomic analysis, revealing varying rates among lineages, positively correlating diversity. Aphid X undergone frequent intra-chromosomal recombination, while autosomes show accelerated inter-chromosomal recombination. Moreover, considering both inter- rearrangements, increased autosomal rearrangement may be common across Aphidomorpha. We identified that expansion DNA transposable elements short interspersed nuclear (SINEs), coupled gene loss duplication associated karyotypic instability (such as RIF1, BRD8, DMC1, TERT), play crucial roles in evolution. Additionally, our analysis revealed mutation detoxification families S. heraclei key factor adapting host plant chemical defenses. Our results provide new insights into evolutionary patterns aphids, aiding understanding diversity adaptive Chromosomal-level comparisons