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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #340404

Research Project: Genetic Dissection of Traits for Sugar Beet Improvement

Location: Sugarbeet and Bean Research

Title: A nine-scaffold genome assembly of the nine chromosome sugar beet

item Mcgrath, J Mitchell - Mitch
item Galewski, Paul - Michigan State University
item Funk, Andy - Michigan State University
item Ou, Shujun - Michigan State University

Submitted to: Annual Beet Sugar Development Foundation Research Report
Publication Type: Research Notes
Publication Acceptance Date: 3/31/2017
Publication Date: 4/1/2017
Citation: McGrath, J.M., Galewski, P., Funk, A., Ou, S. 2017. A nine-scaffold genome assembly of the nine chromosome sugar beet. Annual Beet Sugar Development Foundation Research Report. Denver, Colorado: Beet Sugar Development Foundation. [CD-ROM].

Interpretive Summary:

Technical Abstract: A sugar beet genome sequence is required to take full advantage of the increasingly powerful approaches directed a single nucleotide resolution across the whole genome. A high quality reference genome serves as a benchmark from which other genotypes might be compared and exploited for sugar beet improvement. We assembled the sugar beet genome 'C869', which is the common seed parent for all recombinant inbred populations. Progeny of a five-generation inbred of C869 (aka EL10) were sown in the greenhouse and evaluated for trueness-to-type. PacBio provides long reads of contiguous bases (contigs), these sequences were used as the basis of the current C869 genome sequence. PacBio sequences were assembled with the Falcon Assembler resulting in 938 primary contigs whose length exceeded 40 Kb, and were scaffolded with two optical maps, resulting in a final sequence of 566 Mb. Further, this assembly was scaffolded using Hi-C technology, resulting in an assembly with an equal number of scaffolds as chromosomes.