Cenchrus purpureus and Cenchrus americanus repeatome provide chromosomal markers to distinguish subgenomes

Abstract

Cenchrus L. is an important genus within the family Poaceae, comprising species of agronomic importance, such as C. purpureus and C. americanus. C. americanus is a diploid species (2n = 2x = 14, AA genome), while C. purpureus is an allotetraploid (2n = 4x = 28, A’A’BB genome). The A’ subgenome is proposed to be homeologous to and possibly derived from the A subgenome, while the origin of the B subgenome remains undefined. Despite their distinct subgenomic compositions, both species exhibit a high level of genome homology. This study aimed to characterize and compare the repetitive genome fraction of C. purpureus and C. americanus using genome skimming and a graph-based clustering approach, as well as the in situ hybridization (FISH). The repetitive genome fraction of C. purpureus and C. americanus corresponds to 52.23% and 76.82%, respectively. The most abundant repetitive elements in both species are the LTR retrotransposons. Satellite DNA sequences correspond to 2.55% and 4.17% of the species’ genome, respectively. Four new satellite sequences were identified as A, A’ and B subgenome-specific sequences, along with new centromeric variants. The ancestral relationship and the polyploidization-diploidization cycles played a fundamental role in the composition of their repetitive fraction.