Pangenome analysis reveals transposon-driven genome evolution in cotton

Area of Science:

• Genomics
• Plant Evolution
• Bioinformatics

Background:

• Transposable elements (TEs) are key drivers of plant genome evolution and diversification.
• Pangenomics offers a robust framework to study TE evolution, overcoming intraspecific diversity limitations.

Purpose of the Study:

• To construct a pangenome for diploid A-genome cotton to explore TE dynamics and their impact on genome evolution.
• To identify novel genes and genetic variations associated with geographic distribution and gene expression.

Main Methods:

• Pangenome construction using 344 diploid A-genome cotton accessions.
• Identification of non-reference sequences (NRSs), novel protein-coding genes, and presence-absence variations (PAVs).
• Analysis of transposable element (TE) proliferation patterns and their impact on gene loss and gain.

Main Results:

• A cotton pangenome revealed 511 Mb of NRSs and 5479 new genes.
• Identified 3301 PAVs linked to gene expression, including 2342 novel expression quantitative trait loci (eQTLs) in NRSs.
• Observed distinct TE proliferation in diploid vs. tetraploid cotton, with LTR retrotransposons expanding in polyploids and driving subgenome changes.

Conclusions:

• Pangenome analysis provides critical insights into cotton genomics and subgenome evolution post-polyploidization.
• Demonstrates the utility of pangenome approaches for understanding TE impacts on genome evolution.