Evidence map›Paper›PMID 42191720›Full record

ArticleNature communications2026

Telomere-to-telomere genome assembly of Oryza australiensis reveals transposon-driven centromere repositioning and shared EE-DD ancestry.

Yu Bao, Hanli You, Shuo Liu, Guanqing Liu, Yuechao Wu, Qingqing Yang, Qi You, Peng Liu, Chuandeng Yi, Wenli Zhang and 2 more

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Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Yu Bao *Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Hanli You *Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Shuo LiuJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Guanqing LiuJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Yuechao WuJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Qingqing YangJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Qi YouJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
Peng LiuJoint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China.
Chuandeng YiJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China. cdyi@yzu.edu.cn.
Wenli ZhangNational Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored By Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, China. wzhang25@njau.edu.cn.ORCID http://orcid.org/0000-0003-0710-1966
Zhukuan ChengJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China. zkcheng@genetics.ac.cn.ORCID http://orcid.org/0000-0001-8428-8010
Tao ZhangJiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China. zhangtao@yzu.edu.cn.ORCID http://orcid.org/0000-0002-7897-0205

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Oryza australiensis (EE genome), the sole representative of the EE genome in the genus, holds significant value for deciphering polyploid evolution and mining stress-resistance genes owing to its extreme environmental adaptability. Here, we report a telomere-to-telomere (T2T) genome assembly of O. australiensis, yielding a 901 Mb genome with 12 complete chromosomes. This enables comprehensive annotation of centromeres, telomeres, and 36,742 genes, revealing non-canonical telomeric repeats and three distinct centromere repositioning mechanisms: inversion-driven shifts, duplication-mediated neocentromerization, and transposon burst-induced neocentromere formation. Crucially, transposon dynamics analysis reveals synchronized amplification of Angela LTR retrotransposons in the EE genome and the DD subgenome of allotetraploid O. alta (CCDD) prior to CCDD formation. Phylogenetic and synteny analyses of Angela LTR integrase domains, alongside a 275-bp repeat marker exclusive to EE and DD, indicate that the ancestral lineage that contributed the DD subgenome share common ancestry with an EE-like progenitor. These findings refine Oryza evolutionary history and highlight transposon dynamics in reconstructing deep evolutionary relationships.

Indexed as

CentromereDNA Transposable ElementsGenome, PlantOryzaTelomereChromosomes, PlantEvolution, MolecularPhylogenyPolyploidyRetroelementsDNA Transposable ElementsRetroelements

Identifiers

PMID42191720
PMCPMC13388940

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