Reference Genome for the Highly Transformable <i>Setaria viridis</i> ME034V

Abstract

<i>Setaria viridis</i> (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C₄ photosynthesis. The <i>S. viridis</i> accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous <i>de novo</i> assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for <i>S. viridis</i> Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced <i>Setaria</i> genomes as well as to a diversity panel of 235 <i>S. viridis</i> accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of <i>copia</i> and <i>gypsy</i> LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in <i>Setaria</i>, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in <i>Setaria</i> illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the <i>Setaria</i> research community.