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 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.

Novel QTL associated with Rhizoctonia solani Kühn resistance identified in two table beet × sugar beet F2:3 populations using a new table beet reference genome

“…The Tassel v2 GBS Pipeline (Glaubitz et al., 2014) and Bowtie2 alignment software (Langmead & Salzberg, 2012) were used to align demultiplexed 64 bp forward reads to a draft assembly for table beet, W357B (Dorn, 2022), and sugar beet reference genome, EL10.2‐P01197_ID_57232 (McGrath et al., 2020), for the SBRP and TBRP, respectively. U.S. Department of Agriculture Agricultural Research Service (USDA‐ARS) researchers created a chromosome‐scale assembly for table beet inbred W357B using PacBio Hifi and DoveTail Omni‐C sequencing (K.M.…”

“…McGrath et al. (2020) used a combination of short‐ and long‐read sequencing, physical/optical maps, genetic maps, and Hi‐C chromatin confirmation capture to create the EL10 sugar beet genome assembly. The 540 Mb annotated EL10.1 assembly has 24,255 predicted protein coding regions with a mean of 2,559 coding regions per chromosome.…”

“…The 540 Mb annotated EL10.1 assembly has 24,255 predicted protein coding regions with a mean of 2,559 coding regions per chromosome. Inversions associated with the assembly process itself were resolved, and scaffold placement improved to create EL10.2 (McGrath et al., 2020). Alignment rates of 97.3% and 94.8% were obtained for short‐reads derived from the SBRP and TBRP with the assemblies for W357B and EL10.2, respectively.…”

“…These improvements facilitated the development of a genome assembly for sugar beet inbred EL10 (McGrath et al., 2020). Further improvements to EL10.1 were incorporated and resulted in EL10.2 (McGrath et al., 2020). In some of his work with other Beta crops, J. M. McGrath also self‐pollinated the table beet inbred, W357B, for several generations (Galewski & McGrath, 2020).…”

“…Following the additional inbreeding generations, K. M. Dorn developed a chromosome‐scale assembly for W357B (Dorn, 2022). The EL10.2 and W357B reference assemblies facilitated the construction of linkage maps used in this study (Dorn, 2022; McGrath et al., 2020).…”