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<p>Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for <i>Silphium integrifolium</i> Michx. and <i>S. perfoliatum</i> L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication.</p>

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Assembly of Silphium interspecific hybrid genomes opens the genus to phylogenomics, ecogenomics, and molecular breeding

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月9日

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  • Renan S. Souza,
  • Josh P. Clevenger,
  • Jerry Jenkins,
  • Walid Korani,
  • Jeremy Schmutz,
  • Jane Grimwood,
  • Christopher Plott,
  • Yaniv Brandvain,
  • Kathryn Turner,
  • Allison J. Miller,
  • Brent S. Hulke,
  • Louis F. Nastasi,
  • Ebony G. Murrell,
  • Lori H. Handley,
  • Jenell Webber,
  • Lori Beth Boston,
  • Stella Woeltjen,
  • Matthew J. Rubin,
  • Betsy Trana,
  • Erin Howard,
  • Ashlyn Bazzel,
  • Alex Harkess,
  • David L. Van Tassel

摘要

Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication.