Solyntus, the new highly contiguous reference genome for potato (Solanum tuberosum)

Natascha van Lieshout, Ate van der Burgt, Michiel E. de Vries, Menno ter Maat, David Eickholt, Danny Esselink, Martijn P.W. van Kaauwen, Linda P. Kodde, Richard G.F. Visser, Pim Lindhout, Richard Finkers*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated “DM”, has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/. With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.

Original languageEnglish
Pages (from-to)3489-3495
Number of pages7
JournalG3: Genes, Genomes, Genetics
Volume10
Issue number10
DOIs
Publication statusPublished - Oct 2020

Keywords

  • Diploid breeding
  • Genome assembly
  • Homozygosity
  • Potato
  • Solanum tuberosum

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