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

© 2023 The Authors. Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences..

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 and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 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.

Medienart:

E-Artikel

Erscheinungsjahr:

2024

Erschienen:

2024

Enthalten in:

Zur Gesamtaufnahme - volume:66

Enthalten in:

Journal of integrative plant biology - 66(2024), 2 vom: 30. Feb., Seite 196-207

Sprache:

Englisch

Beteiligte Personen:

Lv, Yang [VerfasserIn]
Liu, Congcong [VerfasserIn]
Li, Xiaoxia [VerfasserIn]
Wang, Yueying [VerfasserIn]
He, Huiying [VerfasserIn]
He, Wenchuang [VerfasserIn]
Chen, Wu [VerfasserIn]
Yang, Longbo [VerfasserIn]
Dai, Xiaofan [VerfasserIn]
Cao, Xinglan [VerfasserIn]
Yu, Xiaoman [VerfasserIn]
Liu, Jiajia [VerfasserIn]
Zhang, Bin [VerfasserIn]
Wei, Hua [VerfasserIn]
Zhang, Hong [VerfasserIn]
Qian, Hongge [VerfasserIn]
Shi, Chuanlin [VerfasserIn]
Leng, Yue [VerfasserIn]
Liu, Xiangpei [VerfasserIn]
Guo, Mingliang [VerfasserIn]
Wang, Xianmeng [VerfasserIn]
Zhang, Zhipeng [VerfasserIn]
Wang, Tianyi [VerfasserIn]
Zhang, Bintao [VerfasserIn]
Xu, Qiang [VerfasserIn]
Cui, Yan [VerfasserIn]
Zhang, Qianqian [VerfasserIn]
Yuan, Qiaoling [VerfasserIn]
Jahan, Noushin [VerfasserIn]
Ma, Jie [VerfasserIn]
Zheng, Xiaoming [VerfasserIn]
Zhou, Yongfeng [VerfasserIn]
Qian, Qian [VerfasserIn]
Guo, Longbiao [VerfasserIn]
Shang, Lianguang [VerfasserIn]

Links:

Volltext

Themen:

CentO satellite repeat
Centromere
DNA, Satellite
Journal Article
Rice
Super pan-genome

Anmerkungen:

Date Completed 22.02.2024

Date Revised 22.02.2024

published: Print-Electronic

Citation Status MEDLINE

doi:

10.1111/jipb.13607

funding:

Förderinstitution / Projekttitel:

PPN (Katalog-ID):

NLM366495232