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

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 drawn from EL10 progeny and three unrelated germplasm accessions, 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.

A roadmap to Durable BCTV Resistance Using Long-Read Genome Assembly of Genetic Stock KDH13

“…This included a high read alignment percentage, clustering based on relationship coefficients, relative proportions nucleotides, and genome assembly size. More in-depth comparisons regarding comparisons between EL10.1 and RefBeet-1.2.2 are available in McGrath et al (2020). Sugar beet genomes share a high degree of genome variation and cluster at the population level (Galewski and McGrath 2020).…”

“…The construction of reference genomes is also evolving; long-read technologies provide solutions to the challenges encountered when assembling highly repetitive plant genomes using short reads. Several reference genomes exist for beet which highlights this progress (Dohm et al 2014;McGrath et al 2020). High-quality reference genomes in beet have provided a lens to measure genome diversity (Galewski and McGrath 2020) as well as assess the content of important functional genes such as those involved in disease resistance (Funk et al 2018).…”

Broken, silent, and in hiding: Tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris)

“…Using these nHMMs with nhmmer (Wheeler and Eddy, 2013), we identified the EPRV RT and MP sequences from the sugar beet EL10.1 assembly (Funk et al, 2018;McGrath et al, 2020) as well as the corresponding single molecule real-time (SMRT) reads (genebank accession SRX3402137). The results were parsed to analyze the hits, choose cut-off parameters and extract the corresponding sequences.…”

“…Reference genome sequences and long read information are already available for two B. vulgaris genotypes (Dohm et al, 2014;Funk et al, 2018;McGrath et al, 2020).…”

Beta vulgaris ssp. vulgaris chromosome 8 shows significant association with geosmin concentration in table beet

“…No table beet genome has been published to date, but because sugar beet shows very close genetic relationship to table beet and is confirmed to contain geosmin ( Tyler et al 1978 ; Freidig and Goldman 2014 ), the genomic tools developed for sugar beet breeding can be leveraged for investigation of the genetic basis of geosmin concentration in table beet. Two sugar beet reference genomes have been published to date: RefBeet ( Dohm et al 2014 ) from short Illumina-derived DNA sequences and EL10 ( Funk et al 2018 ; McGrath et al 2020 ) from PacBio long DNA reads, optical mapping, and Hi-C reads. EL10 versions EL10.1 and EL10.2 comprise nine main scaffolds, along with 31 and 9 additional small scaffolds, respectively.…”