Genome report: a draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

Abstract

The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

Direct and indirect fitness effects of plant metabolites and genetic constraints limit evolution of allelopathy in an invading plant

“…Four of the 23 seed families did not produce viable seeds, and were replaced with seeds grown from the original field collection (Figure 1; Table 1). This includes one genotype from the native range (EFCC2-4-80), which was included because it is from a source population close to the genotype used in the garlic mustard genome project (Alabi et al 2021). However, excluding it from the final analysis did not appreciably change any of the results presented.…”

“…Alliaria petiolata (garlic mustard) is emerging as a model system for integrated studies in invasion biology (Kueffer et al 2013;Colautti et al 2014;Alabi et al 2021). Native to much of Eurasia, it was first recorded in North America in 1868 in Long Island, New York .…”

“…The biennial herb Alliaria petiolata (garlic mustard) is an emerging model system in ecological genetics (Alabi et al 2021) with relevance to broader questions about the role of ecological interactions in the rapid evolution and spread of invasive species (Rodgers et al 2022). A member of the mustard family (Brassicaceae), A. petiolata is native to Eurasia and invading forest understories of North America, where it can be an aggressive weed (Rodgers et al 2008).…”

Technology-enabled great leap in deciphering plant genomes

“…Meanwhile, multiple software developed using different algorithms offer us the opportunity to create more complete assembly 14 . From Velvet 15 , ABySS 16 , AllPath-LG 17 , and SOAPdenovo 18 contig assemblers by short reads to Canu 19 , Mecat2 20 , Necat 21 , Falcon 22 by TGS technologies, more high-quality genomes have been assembled. Hi asm, a software using HiFi reads as input for contig assembly, has been applied in generating haplotype-resolved de novo assembly, even telomere-to-telomere (T2T) assembly when combining HiFi reads with ultra-long ONT reads 5,23 .…”

Where Is Garlic Mustard? Understanding the Ecological Context for Invasions of Alliaria petiolata

“…Bieb.) Cavara and Grande (garlic mustard, Brassicaceae) is often used as a model or case study for plant invasion because it currently has a wide distribution, is considered a primary threat to hardwood forests, has been widely studied (Barney and Whitlow 2008 , Colautti et al 2014 ), and has recently had its genome sequenced (Alabi et al 2021 ), which makes it an ideal species to elucidate the influence of ecological context on invasion success. As a western Eurasian plant, garlic mustard was likely introduced to North America by early colonists as a medicinal plant and garlic substitute (Grieve 1959 ).…”