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To reconstruct the gene orders of the constituent genomes in an ancestral pangenome, we propose an analysis of raccroche maximum weight matching output of contigs based on adjacency pairs from phylogenetically disparate genomes. The key idea is to use the multiple solutions to the matching optimization as a sample of the set of constituent genomes. We identify those gene-order contigs present in all the solutions as the “core” of the pangenome, and those absent in some of the solutions as the pangenome “shell”. Different cliques of mutually compatible shell contigs identified different constituent genomes. A significant proportion of shell genes in each pangenome was inherited from the set of shell genes in its ancestor pangenome. As a hint to the chromosomal structure, we performed hierarchical clustering on the combined set of contigs based on the number of solutions shared by each pair of contigs, in the search for chromosomal fragments, large clusters present in many ancestors, and some limited but clear results were obtained.

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Reconstructing the Constituent Genomes of the Ancestral Angiosperm Pangenome

  • 会议论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年

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  • David Sankoff,
  • Jiazhen Leng,
  • Pratheesh Soman,
  • Qiaoji Xu,
  • Chunfang Zheng,
  • Alex Liu,
  • James H. Leebens-Mack,
  • Lingling Jin

摘要

To reconstruct the gene orders of the constituent genomes in an ancestral pangenome, we propose an analysis of raccroche maximum weight matching output of contigs based on adjacency pairs from phylogenetically disparate genomes. The key idea is to use the multiple solutions to the matching optimization as a sample of the set of constituent genomes. We identify those gene-order contigs present in all the solutions as the “core” of the pangenome, and those absent in some of the solutions as the pangenome “shell”. Different cliques of mutually compatible shell contigs identified different constituent genomes. A significant proportion of shell genes in each pangenome was inherited from the set of shell genes in its ancestor pangenome. As a hint to the chromosomal structure, we performed hierarchical clustering on the combined set of contigs based on the number of solutions shared by each pair of contigs, in the search for chromosomal fragments, large clusters present in many ancestors, and some limited but clear results were obtained.