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. Oryza australiensis (EE genome) is a wild rice species with extreme environmental adaptability and grain properties. Here, the authors report its telomere-to-telomere genome assembly and clarify that the ancestral lineage that contributed the DD subgenome shared common ancestry with an EE-like progenitor.
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Claims 8
Claim · model-written summary
A telomere-to-telomere assembly yielded a 901 Mb O. australiensis genome with 12 complete chromosomes.
- Taxon
- O. australiensis
Oryza australiensise0 - Outcome
- genome assemblye0
- Value
- 901 Mbe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“telomere-to-telomere (T2T) genome assembly of O. australiensis, yielding a 901 Mb genome with 12 complete chromosomes.”
Claim · model-written summary
The assembly enabled annotation of 36,742 genes.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- annotation of centromeres, telomeres, and 36,742 genese0
- Value
- 36,742 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“This enables comprehensive annotation of centromeres, telomeres, and 36,742 genes”
t0“Oryza australiensis”
Claim · model-written summary
Non-canonical telomeric repeats were found in O. australiensis.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- non-canonical telomeric repeatse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“revealing non-canonical telomeric repeats”
t0“Oryza australiensis”
Claim · model-written summary
Centromere repositioning involved inversion-driven shifts.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- inversion-driven shiftse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“three distinct centromere repositioning mechanisms: inversion-driven shifts, duplication-mediated neocentromerization, and transposon burst-induced neocentromere formation”
t0“Oryza australiensis”
Claim · model-written summary
Centromere repositioning involved duplication-mediated neocentromerization.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- duplication-mediated neocentromerizatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“duplication-mediated neocentromerization”
t0“Oryza australiensis”
Claim · model-written summary
Centromere repositioning involved transposon burst-induced neocentromere formation.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- transposon burst-induced neocentromere formatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“transposon burst-induced neocentromere formation”
t0“Oryza australiensis”
Claim · model-written summary
Angela LTR retrotransposons amplified synchronously in EE and DD before CCDD formation.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- synchronized amplification of Angela LTR retrotransposonse0
- Qualifier
- prior to CCDD formatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“synchronized amplification of Angela LTR retrotransposons in the EE genome and the DD subgenome of allotetraploid O. alta (CCDD) prior to CCDD formation.”
t0“Oryza australiensis”
Claim · model-written summary
The DD ancestral lineage shared ancestry with an EE-like progenitor.
- Taxon
- Oryza australiensisOryza australiensist0
- Outcome
- share common ancestry with an EE-like progenitore0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the ancestral lineage that contributed the DD subgenome share common ancestry with an EE-like progenitor.”
t0“Oryza australiensis”