Exploring the Satellitome of the Pest Aphid Acyrthosiphon pisum (Hemiptera, Aphididae): Insights Into Genome Organization and Intraspecies Evolution

Abstract

Satellite DNAs (satDNAs), ubiquitous sequences in eukaryotic genomes, play a crucial role in genome organization, function, and evolution. The pea aphid Acyrthosiphon pisum is a major crop pest, and an emerging model for ecological, developmental, and evolutionary studies. This study characterizes the satellitome of the A. pisum to better understand its genomic organization and the evolutionary dynamics of satDNAs at the intraspecies level. The analysis of satDNAs across various host-plant adapted biotypes reveals a general sharing of the satellitome, with significative quantitative differences. We observe the amplification or contraction of specific satDNA families, even in the same biotype, consistent with the fast-evolutionary changes characteristic of these sequences. Rapid differential accumulation of repetitive elements among biotypes together with other factors may contribute to the origin of genetic incompatibilities. At the interspecific level, fluctuations in satDNA abundances, including the loss of certain families, are consistent with the library hypothesis, long-term conservation, and differential amplification of an ancestral satellitome. SatDNAs are considerably enriched in the heterochromatin of the chromosome X (Chr-X) and to a less extent, dispersed across the euchromatic region of all chromosomes. The enrichment of these sequences on Chr-X also features the elements that are most recently amplified and homogenized. This suggests that Chr-X could serve as a fountain of youth for satDNAs, contributing to the "fast-X" effect. Our findings provide valuable insights into genome structure, assembly, and the potential impact of satDNAs on species diversification, as well as the evolution of autosomes and Chr-X.