Pangenome analysis reveals transposon-driven genome evolution in cotton

Abstract

Background Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. Results Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. Conclusions Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.

Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding

“…This allows breeders to harness core genome variation and rare variation in each material, thereby providing genetic resources to enhance traits such as yield, quality, resistance, and adaptability ( Abbas et al., 2022 ). In 2021, the inaugural cotton pan-genome of allotetraploid cotton was released, featuring the most diverse variation data-set to date, followed by the pangenome of diploid cotton species ( Wang et al., 2022 ; He et al., 2024 ). It sheds light on the genomics foundations of cotton domestication and improvement across multiple scales, offering valuable insights into essential cotton traits from a pan-genome perspective ( Li et al., 2021 ).…”