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Key message <p>Comparative analysis of 40 diploid cotton genomes reveals contrasting evolutionary patterns among gene duplication modes, linking WGD/DSD to conserved functions and TD/PD/TRD to rapid diversification.</p> Abstract <p>The increasing availability of high-quality cotton genomes and developmental time-course transcriptomes datasets has facilitated comparative analyses of gene duplication during cotton evolution. However, the evolutionary characteristics of different duplication modes in diploid cotton remain incompletely understood. In this study, we analyzed 40 diploid cotton genomes and transcriptome datasets from representative diploid and tetraploid cottons species to compare five duplication modes, including whole-genome duplication (WGD), tandem duplication (TD), proximal duplication (PD), transposed duplication (TRD), and dispersed duplication (DSD). The results showed that DSD and WGD are the primary drivers of diploid cotton genome architecture, although their contributions vary significantly among species. Most duplicated genes evolved under purifying selection, with WGD- and DSD-derived genes generally exhibiting lower <i>Ka/Ks</i> values than TD-, PD-, and TRD-derived genes. Transcriptome analysis further indicated that WGD genes exhibit the highest expression conservation during seed development, whereas TD and TRD genes showed greater expression divergence. In particular, TD gene expression divergence was observed between diploid progenitors and became more pronounced following polyploidization and domestication. Gene conversion patterns also differed among duplication modes. TD-derived genes exhibited relatively frequent and persistent gene conversion events, likely associated with the close physical distance between duplicated gene copies. By contrast, gene conversion was less common in other duplication categories. Overall, these findings suggest that different duplication modes contributed differently to cotton genome evolution and functional divergence. WGD- and DSD-derived genes appear to be associated with relatively conserved evolution, whereas TD-, PD-, and TRD-derived genes may contribute more to functional diversification and adaptive evolution in cotton. These results provide useful insights into duplicated gene evolution and genome diversification in cotton.</p>

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Distinct evolutionary trajectories of gene duplication modes in 40 diploid cotton genomes

  • 期刊论文

  • 发表日期：

    2026年6月20日

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  • Chao Shen,
  • Jiaxin Wu,
  • Wenxi Huang,
  • Menghan Yang,
  • Lejun Ouyang,
  • Yongguo Zhao,
  • Guangyuan Lu

摘要

Key message

Comparative analysis of 40 diploid cotton genomes reveals contrasting evolutionary patterns among gene duplication modes, linking WGD/DSD to conserved functions and TD/PD/TRD to rapid diversification.

Abstract

The increasing availability of high-quality cotton genomes and developmental time-course transcriptomes datasets has facilitated comparative analyses of gene duplication during cotton evolution. However, the evolutionary characteristics of different duplication modes in diploid cotton remain incompletely understood. In this study, we analyzed 40 diploid cotton genomes and transcriptome datasets from representative diploid and tetraploid cottons species to compare five duplication modes, including whole-genome duplication (WGD), tandem duplication (TD), proximal duplication (PD), transposed duplication (TRD), and dispersed duplication (DSD). The results showed that DSD and WGD are the primary drivers of diploid cotton genome architecture, although their contributions vary significantly among species. Most duplicated genes evolved under purifying selection, with WGD- and DSD-derived genes generally exhibiting lower Ka/Ks values than TD-, PD-, and TRD-derived genes. Transcriptome analysis further indicated that WGD genes exhibit the highest expression conservation during seed development, whereas TD and TRD genes showed greater expression divergence. In particular, TD gene expression divergence was observed between diploid progenitors and became more pronounced following polyploidization and domestication. Gene conversion patterns also differed among duplication modes. TD-derived genes exhibited relatively frequent and persistent gene conversion events, likely associated with the close physical distance between duplicated gene copies. By contrast, gene conversion was less common in other duplication categories. Overall, these findings suggest that different duplication modes contributed differently to cotton genome evolution and functional divergence. WGD- and DSD-derived genes appear to be associated with relatively conserved evolution, whereas TD-, PD-, and TRD-derived genes may contribute more to functional diversification and adaptive evolution in cotton. These results provide useful insights into duplicated gene evolution and genome diversification in cotton.