Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Abstract

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

Keywords: comparative genomics; genetic mapping; genome annotations; genome assembly; pennycress.

Figure 1

Overview of the seven largest scaffolds representing chromosomes in T. arvense var. MN106‐Ref. The tracks denote (a) DNA methylation level in shoot tissue (CG: grey; CHG: black; CHH: pink; 200 kbp window size), and density distributions (1 Mbp window size) of (b) protein‐coding loci, (c) sRNA loci, (d) Gypsy retrotransposons, (e) Copia retrotransposons, (f) LTR retrotransposons and (g) pseudogenes.

Figure 2

Distribution of ancestral genomic blocks (top panel) along the seven largest scaffolds of T. arvense MN106‐Ref (T_arvense_v2), and a comparison of these genomic blocks with Eutrema salsugineum, Schrenkiella parvula, Arabidopsis thaliana and Arabidopsis lyrata.

Figure 3

Feature annotations within T. arvense var MN106‐Ref. (a) Rooted species tree inferred from all genes, denoting node support and branch length in substitutions per site, and horizontal stacked bar chart comparing the genetic fraction in pennycress with other Brassicaceae sp. (ns = nonspecific orthologs, ss = species‐specific orthologs, un = unclassified genes, nc = non‐coding/intergenic fraction). (b) Comparison of gene macrosynteny between v1 and v2 of the genome, and a microsynteny example of genes MYB29 and MYB76, which are resolved in the v2 annotation. (c) Small RNA biogenesis locus length and expression values in each of four tissues. (d) Overall repetitive content in the genome as discovered by RepeatMasker2, and relative abundance of TEs within the fraction of repetitive elements.

Figure 4

Regulatory dynamics in pennycress. (a) Relative fraction of genes in each tissue for low (0–0.2), intermediate (0.2–0.8) and high/absolute specificity (0.8–1.0) subsets. (b) Log₂(TMM) expression values of the top 30 most highly expressed genes in each tissue, relative to the mean across all tissues, from the subset of genes with a high/absolute tau specificity score. (c) Distribution of average DNA methylation for different genomic features, by cytosine sequence context. (d) DNA methylation along genes (top) and TEs (bottom), including a 2‐kb flanking sequence upstream and downstream. DNA methylation was averaged in non‐overlapping 25‐bp windows.

Figure 5

(a) Dendrogram representing the forty wild accessions in our study showing three distinct subpopulations, inferred from STRUCTURE analysis (Figure S13). (b,c) Variation of transcript isoforms for MN108 (b) and Spring32‐10 (c) accessions based on SQANTI3 analysis. (d) A pale phenotype segregating in an improved pennycress line (fae‐1‐1/rod1‐1) was analysed with a modified bulked‐segregant analysis, and the QTL region associated with this phenotype was mapped using the MutMap approach.