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Post-polyploidization centromere evolution in cotton.

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Summary
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A complete telomere-to-telomere (T2T) genome assembly of Upland cotton (Gossypium hirsutum) reveals centromere evolution. Centromere-associated repetitive sequences (CRCs) were transferred and proliferated, shaping the dynamic centromeric landscape after polyploidization.

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Area of Science:

  • Genomics
  • Plant Biology
  • Evolutionary Biology

Background:

  • Upland cotton (Gossypium hirsutum) is a vital allotetraploid crop, representing over 90% of global production and serving as a model for polyploid domestication.
  • Understanding the genomic architecture and evolution of polyploid crops is crucial for agricultural advancements.

Purpose of the Study:

  • To generate a complete telomere-to-telomere (T2T) genome assembly of Upland cotton (Gossypium hirsutum) accession Texas Marker-1 (T2T-TM-1).
  • To investigate interspecific centromere divergence and the dynamics of centromere-associated repetitive sequences (CRCs) in Upland cotton.

Main Methods:

  • High-quality telomere-to-telomere (T2T) genome sequencing and assembly of Upland cotton (Gossypium hirsutum) T2T-TM-1.
  • Comparative genomics analysis to detect centromere divergence between subgenomes and diploid progenitors.
  • Bioinformatic analysis of centromere-associated repetitive sequences (CRCs) and their evolutionary history.

Main Results:

  • A comprehensive T2T genome assembly of Upland cotton (T2T-TM-1) was achieved, totaling 2,299.6 Mb with 79,642 annotated genes.
  • Interspecific centromere divergence was identified between the A- and D-subgenomes and their diploid progenitors.
  • Centromere-associated repetitive sequences (CRCs), enriched for Gypsy-like retroelements, exhibited expansion, repositioning, and structural variations post-polyploidization, with evidence of transfer and proliferation from the D-genome progenitor.

Conclusions:

  • The complete T2T genome assembly provides a foundational resource for Upland cotton research.
  • Centromere evolution in Upland cotton is characterized by dynamic changes and the significant role of CRCs, particularly those originating from the D-genome progenitor.
  • The findings offer insights into the evolutionary mechanisms shaping centromeric landscapes in polyploid species.