Location: Sugarbeet and Bean ResearchTitle: Assembling a draft genome sequence of USDA germplasm release 'C869' Author
|Mcgrath, J Mitchell - Mitch|
Submitted to: Annual Beet Sugar Development Foundation Research Report
Publication Type: Research Notes
Publication Acceptance Date: 5/1/2014
Publication Date: 6/1/2014
Citation: McGrath, J.M., Townsend, B. 2014. Assembling a draft genome sequence of USDA germplasm release 'C869'. [CD-ROM]. 2013 Annual Beet Sugar Development Foundation Research Report. Denver, Colorado: Beet Sugar Development Foundation. Interpretive Summary:
Technical Abstract: Creation of a high-quality draft 'reference' sequence for the common seed parent for all of East Lansing RIL populations, 'C869', is required to orient segregating, sequence-derived, genetic markers as well as identify genes controlling agronomic production traits in sugar beet. We obtained ~185-fold (post-QC) coverage of the 750 Mega-base pair (Mbp) sugar beet genome with Illumina short reads (paired-end 100 bp sequences) from a single inbred, homozygous plant (EL-A025943-17) and assembled these reads using ABySS (bcgsc.ca/platform/bioinfo/software/abyss) into ~130,000 fragments (contigs) of the beet genome, containing most of the gene space. The maximum contig (i.e. contiguously assembled sequence from short reads) was 75,288 nucleotides (nt) in length and the minimum was 61 nt, with an N50 (median sequence length) of 7,778 nt. This draft assembly was named C869UK_0.1. Of the 38,231 contigs with greater than 10,000 nt, ~30,500 genes were predicted using the MAKER annotation pipeline (yandell-lab.org), which included 18,870 protein coding genes. We also obtained mate-pair reads using the same Illumina technology that span 3 kilobase (kb) (5,985,198 post-QC passed read pairs), 6 kb (1,448,364 post-QC passed read pairs), and 10 kb (139,325 post-QC passed read pairs) regions of the beet genome, and used these to link contigs into larger scaffolds using SSPACE software (baseclear.com). This resulted in a decrease in the number of sequences representing the beet genome from 130,398 fragments of the C869UK_0.1 assembly (above) to 54,793 fragments in this C869UK_0.3 assembly. The sum of nucleotides in the latest assembly was 535,321,901 nt, or approximately 71.4% of the 750 Mbp total genome size of sugar beet, with a maximum scaffold size of 628,544 nt, average scaffold size of 9,769 nt, and a N50 of 50,072 nt.