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Background <p><i>Proserpinaca palustris</i>, a representative heterophyllous plant, represents an emerging model for studying morphological plasticity and adaptive evolution in amphibious environments. However, the absence of a high-quality reference genome has hindered molecular investigations into its heterophylly regulation mechanisms.</p> Results <p>Here, we present the first chromosome-level genome assembly of <i>P. palustris</i>. The final assembly spans 385.32&#xa0;Mb, anchored onto seven pseudochromosomes (1n = 7), and encodes 22,756 predicted protein-coding genes. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment demonstrated high completeness, with scores of 95.61% for the genome assembly and 96.43% for the gene set. Comparative genomic analyses revealed that <i>P. palustris</i> underwent only the ancient <i>γ</i> whole-genome triplication (<i>γ</i>-WGT) event, with no subsequent whole-genome duplication (WGD). Nevertheless, the genome has experienced extensive re-diploidization, likely facilitated by structural rearrangements. Transcriptomic profiling identified three <i>KNOTTED1-like homeobox (KNOX)</i> genes (i.e., <i>PPA02C1640</i>, <i>PPA03C1159</i>, and <i>PPA01C1293</i>) that were significantly differentially expressed between submerged and terrestrial leaves in <i>P. palustris</i>, suggesting their potential role in regulating heterophylly.</p> Conclusions <p>This study provides the first high-quality genomic resource for the genus <i>Proserpinaca</i> (Haloragaceae) and identifies key <i>KNOX</i> genes implicated in heterophylly regulation in <i>P. palustris</i>.</p>

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Chromosome-level genome of Proserpinaca palustris reveals key KNOX genes related to heterophylly formation

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月17日

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  • Yanjing Dong,
  • Qian Qin,
  • Fengqin Li,
  • Zhonghua Tu,
  • Chengyi Tang

摘要

Background

Proserpinaca palustris, a representative heterophyllous plant, represents an emerging model for studying morphological plasticity and adaptive evolution in amphibious environments. However, the absence of a high-quality reference genome has hindered molecular investigations into its heterophylly regulation mechanisms.

Results

Here, we present the first chromosome-level genome assembly of P. palustris. The final assembly spans 385.32 Mb, anchored onto seven pseudochromosomes (1n = 7), and encodes 22,756 predicted protein-coding genes. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment demonstrated high completeness, with scores of 95.61% for the genome assembly and 96.43% for the gene set. Comparative genomic analyses revealed that P. palustris underwent only the ancient γ whole-genome triplication (γ-WGT) event, with no subsequent whole-genome duplication (WGD). Nevertheless, the genome has experienced extensive re-diploidization, likely facilitated by structural rearrangements. Transcriptomic profiling identified three KNOTTED1-like homeobox (KNOX) genes (i.e., PPA02C1640, PPA03C1159, and PPA01C1293) that were significantly differentially expressed between submerged and terrestrial leaves in P. palustris, suggesting their potential role in regulating heterophylly.

Conclusions

This study provides the first high-quality genomic resource for the genus Proserpinaca (Haloragaceae) and identifies key KNOX genes implicated in heterophylly regulation in P. palustris.