The Genome of Apera spica-venti: A Major Grass Weed

Abstract

Apera spica-venti (loose silky bent, or common windgrass) is a diploid grass-weed endemic to Europe and north Asia that has spread to the United States and Canada. This species has become a major grass weed in winter cereals, especially in eastern Europe mainly through the evolution of target site and nontarget site resistance mechanisms. The scientific community currently lacks genomic resources to understand herbicide resistance evolution in this plant and therefore resistance is hard to diagnose and treat. To remedy this, we generated two reference haplome assemblies through phased genome assembly. Haplome 1 consists of 37 scaffolds with a total length of 4.06 Gbp and an N50 of 206.5 Mbp, while haplome 2 resulted in 34 scaffolds with a total length of 3.99 Gbp and an N50 of 270.1 Mbp. Both haplomes represent over 87% of the flow cytometry estimated genome size of 4.622 Gbp per 1C. Gene annotation was performed via a modified Maker pipeline resulting in 44,208 and 43,844 genes for haplomes 1 and 2, respectively, and capturing 90% of BUSCO annotated transcripts. Repeat analysis identified greater than 800,000 transposon elements spanning 2.3 Gbp of the genome and an average distance between genes of over 90 kbp. This reference genome addresses the lack of genomic resources and aims to better understand basic weed biology, ecology, and herbicide resistance evolution.

Keywords: Apera spica-venti; genomes; grass; herbicide; weeds.