DOI: 10.5061/dryad.wstqjq2x5
title: FC309 genome assembly and annotation files

description: Sugar beet (Beta vulgaris L.) is a global source of table sugar and animal
 fodder. Here we report a highly contiguous, haplotype phased genome
 assembly and annotation for sugar beet line FC309. Both assembled haplomes
 for FC309 represent the largest and most contiguous assembled beet genomes
 reported to date, as well as gene annotations sets that capture over 1,500
 additional protein-coding loci compared to prior beet genome annotations.
 These new genomic resources were used to identify novel quantitative trait
 loci (QTL) for Fusarium yellows resistance from the FC309 genetic
 background using an F2 mapping-by-sequencing approach. The highest QTL
 signals were detected on Chromosome 3, spanning approximately 10Mbp in
 both haplomes. A parallel transcriptome profiling experiment identified
 candidate genes within the Chromosome 3 QTL with plausible roles in
 disease response, including NBS-LRR genes with expression trends
 supporting a role in resistance. Investigation of genetic variants in
 these candidate genes found 1 major disease-resistance protein containing
 high-effect variants of interest. Collectively, the genomic resources for
 FC309 presented here are foundational tools for comparative genomics,
 mapping other traits in the FC309 background, and as a reference genome
 for other beet studies due to its contiguity, completeness, and
 high-quality gene annotations.
description: High molecular weight DNA was isolated from a single plant from
 the FC309 sugar beet line for PacBio HiFi sequencing. Young, dark treated
 leaf tissue was collected from the same plant for DoveTail Omni-C
 proximity ligation library preparation and Illumina sequencing. PacBio
 HiFi and DoveTail Omni-C reads were assembled using the software package
 Hifiasm to produce a phased contig level assembly. The two phased contig
 level assemblies were scaffolded using the DoveTail HiRise method to break
 mis-joined contigs and anchor/orient contigs into psuedochromosomes. The
 final assemblies, named USDA_Bvulg_FC309_v1.1 (haplome 1) and
 USDA_Bvulg_FC309_v1.2 (haplome 2) were independently annotated to identify
 and mask repetivie regions of the genome and identify protein coding loci
 using the GenSAS genome annotation pipeline. 
description: # FC309 genome assembly and annotation files
 [https://doi.org/10.5061/dryad.wstqjq2x5](https://doi.org/10.5061/dryad.wstqjq2x5) ## Description of the data and file structure Genome assembly and annotation files for sugar beet line FC309 developed as described in Todd et al. "A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium yellows resistance QTL" published in DNA Research.  ### Files and variables #### File: FC309.zip **Description:** Two directories containing genome assembly and annotation files for FC309 haplome 1 (v1.1.0) and FC309 haplome 2 (v1.2.0). Each haplome directory contains the assembly file (in FASTA format, USDA_Bvulg_FC309_v1.X.0.fasta), genome annotation file (GFF3 format, Masked-FC309v1.X.0-extra-contigs-publish.gff3) which contains the genomic coordinates of final protein coding loci, and both nucleotide (Masked-FC309v1.X.0-extra-contigs-publish.CDS.fna and Masked-FC309v1.X.0-extra-contigs-publish.genes.fna) and and protein sequences for each of the annotated protein coding genes (Masked-FC309v1.X.0-extra-contigs-publish.protein.faa). In each directory, there is also a readme file that describes the genome annotation pipeline that was used.  ## Usage Notes All files are (fasta and gff) are text files that are able to be opened using any text file viewer by appending the file name with ".txt". These files can also be viewed using open source tools like Artemis (https://sanger-pathogens.github.io/Artemis/Artemis/) or JBrowse (https://jbrowse.org/jb2/).  ##