A centromere map based on super pan‐genome highlights the structure and function of rice centromeres

Abstract

Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high‐quality centromere map based on the rice super pan‐genome consisting of a 251‐accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy‐type LTRs, are abundant in the peripheral CentO‐enriched regions (CoERs) and drive rice centromere expansion and evolution. Furthermore, high‐quality genome assembly and complete T2T reference genome enable us to obtain more centromeric genome information despite the mapping and cloning of centromere genes is challenging. We investigated the association between structural variations (SVs) and gene expression in the rice centromere. A centromere gene, OsMAB, that positively regulates rice tiller number, was further confirmed by eQTL, haplotype analysis and CRISPR/Cas9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.This article is protected by copyright. All rights reserved.

Characterization of the CsCENH3 protein and centromeric DNA profiles reveal the structures of centromeres in cucumber

“…S8 ). Recently, researchers identified a centromeric gene, AGIS_Os12g018490 ( OsMAB ), using eQTL and haplotype analysis, which plays a role in regulating tiller number in rice [ 11 ]. Several studies have also reported transcriptional activity in centromeric regions in plants and other species [ 52–54 ].…”

“…The length and distribution of satellite repeats are species-specific [ 7 ]. For instance, CentO satellite repeats consist mainly of 155- and 165-bp monomers, which have been identified throughout a super pan-genome in rice [ 11 ]. Additionally, the Arabidopsis pan-centromere was found to contain two satellite repeats, AthCEN178 (~178 bp, formerly known as CEN180) and AthCEN159 (159 bp, formerly known as CEN160), which are mainly monomers in Arabidopsis [ 12 ].…”

“…In Arabidopsis , transcription of more than 47 genes has been detected around the core centromeric region that contains CEN180 repeats [ 22 ]. In addition, there are 11 genes with transcriptional activity at the centromere of the maize chromosome [ 23 ], while the centromeres have at least 4 active genes in rice [ 11 , 24 ]. Although telomere-to-telomere gene assembly has been completed in humans [ 25 ], maize [ 26 ], soybean [ 27 ], and other species [ 28 , 29 ] in recent years, the complete assembly of centromeric regions, which are rich in satellite repeats, remains a challenge.…”