Centromeric repeats in Citrus sinensis provide new insights into centromeric evolution and the distribution of G-quadruplex structures

Abstract

Centromeres play a crucial role in ensuring the accurate separation of chromosomes during cell division. Despite the three rounds of genome sequencing technology undergone by Citrus sinensis (sweet orange), the presence of numerous repetitive DNA elements in its genome has led to substantial gaps in centromeric genomic mapping, leaving the composition of centromeric repeats unclear. To address this, we employed a combination of chromatin immunoprecipitation sequencing with the C. sinensis centromere-specific histone H3 variant antibody and centromere-specific bacterial artificial chromosome-3a sequencing to precisely locate the centromeres. This approach allowed us to identify a series of centromere-specific repeats, comprising five tandem repeats and nine long terminal repeat retrotransposons. Through comprehensive bioinformatics analysis, we gained valuable insights into potential centromeric evolution events and discovered the presence of DNA G-quadruplex structures of centromeric repeats in C. sinensis. Altogether, our study not only offers a valuable reference for centromeric genome assembly but also sheds light on the structural characteristics of C. sinensis centromeres.