From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

Vargas-Mejia, P.; Gutierrez-Manriquez, C.; Anderson, E. S.; Williams, D. R.; Vega-Arreguin, J. C.; Fresnedo Ramirez, J.

doi:10.64898/2026.10.23.761435

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bioRxiv · 10.64898/2026.10.23.761435

From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits

Vargas-Mejia, P.·Gutierrez-Manriquez, C.·Anderson, E. S.·Williams, D. R.·Vega-Arreguin, J. C.·Fresnedo Ramirez, J.

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Abstract

Natural rubber supply depends almost entirely on one tropical tree, motivating development of temperate alternatives. Rubber dandelion (Taraxacum kok-saghyz Rodin) is the leading candidate, with comparatively well characterized rubber biosynthesis pathways, but its large, repeat-rich genome has left breeding genomics far behind pathway biology. In response, we assembled OSU TarKok 3.0, a 1.19-Gb nuclear reference in which eight chromosome-scale scaffolds contain 98% of the sequence. Continuity within chromosomes improved markedly, with contig N50 rising from 1.3 to 37.8 Mb, and conserved gene-space recovery improved accordingly. Macrosynteny showed strong chromosome conservation within Taraxacum and, when compared to lettuce, displayed four nearly intact and four composite chromosomes, a signature compatible with descending dysploidy accompanied by rearrangement rather than a single end-to-end fusion. Across nine Cichorieae genomes, none of six surveyed rubber-related gene families was uniquely enlarged in rubber dandelion. Instead, a cis-prenyltransferase locus, a rubber transferase activator, and three small rubber particle protein genes were enriched in underground tissues and grouped with rubber elongation factor in a latex-associated co-expression module, favoring coordinated pathway deployment over species-specific family expansion. Intersecting uniquely mappable and nonrepetitive sequence defined the mappable genome, approximately 210 Mb or 18% of the assembly, within which markers can be interpreted allelically. Mapping in an independent F2 family of 83 plants identified a chromosome 1 locus for filled-seed production under restricted cross-pollination, whereas herbicide response yielded no significant locus in this design. OSU TarKok 3.0 links chromosome reorganization, pathway deployment, and domestication traits into one framework for improving an outcrossing crop.

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Vargas-Mejia, P., Gutierrez-Manriquez, C., Anderson, E. S., Williams, D. R., Vega-Arreguin, J. C., Fresnedo Ramirez, J.. 2026-10-27. From chromosome-scale assembly to the mappable genome of rubber dandelion: chromosome reorganization, rubber-pathway coordination, and domestication traits. https://doi.org/10.64898/2026.10.23.761435

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