A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

Authors: McGrath, Jon; FUNK, ANDY - Michigan State University; GALEWSKI, PAUL - Michigan State University; OU, SHUJUN - Michigan State University; TOWNSEND, BELINDA - Rothamsted Research; DAVENPORT, KAREN - Los Alamos National Research Laboratory; DALIGAULT, HAJNALKA - Los Alamos National Research Laboratory; JOHNSON, SHANNON - Los Alamos National Research Laboratory; LEE, JOYCE - Bionano Genomics, Inc; HASTIE, ALEX - Bionano Genomics, Inc; Naegele, Rachel; Dorn, Kevin

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2022
Publication Date: 10/8/2022
Citation: McGrath, J.M., Funk, A., Galewski, P., Ou, S., Townsend, B., Davenport, K., Daligault, H., Johnson, S., Lee, J., Hastie, A., Naegele, R.P., Dorn, K.M. 2022. A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.). DNA Research. 30(1). Article edsac033. https://doi.org/10.1093/dnares/dsac033.
DOI: https://doi.org/10.1093/dnares/dsac033

Interpretive Summary: Beets are cultivated for leaf and root vegetables, animal fodder, and up to 30% of the world’s refined sucrose. A reference-quality assembly of the inbred ‘EL10’ sugar beet genome was constructed using third generation sequence and assembly tools and was contained in the nine chromosomes of beets. Variation in genome size was investigated, producing estimates from 633 to 875 Mb. Mapping with short-read whole genome sequences from other germplasm revealed relatively few regions of the sugar beet genome associated with very high-copy number variation. Gene annotation incorporating curated sequences generated 24,255 gene models. Duplicate gene analyses revealed little large-scale duplication and reduced gene copy number for well-annotated gene families, especially transcription factors. The results of these analyses indicate that the EL10.1 genome assembly is a highly contiguous, consistent genome assembly that provides a new resource for improvement of B. vulgaris, as well as provides additional opportunities to investigate broader comparative genomics across the plant kingdom.

Technical Abstract: A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short read error correction. The EL10.1 assembly was 540 Mb, of which 96.7% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNAseq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read depth mapping with short-read whole genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.