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

Abstract

Summary 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.

Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense

“…The species is an interesting study object also because it is currently being domesticated into a new biofuel and cover crop [37][38][39][40][41]. The genomic work with T. arvense is facilitated by recently published high-quality reference genomes [36,42]. In our study, we demonstrate that European populations of T. arvense harbour substantial natural epigenetic variation, which is associated with DNA sequence variation as well as with climate of origin, but in a highly contextdependent manner.…”

“…We not only distinguished PLOS GENETICS between the three sequence contexts CG, CHG and CHH, but we also assigned cytosines to different genomic features: CDS, introns, promoters, TEs and intergenic regions. For genes and TEs, we used available annotations [36], while for promoters we considered the 2 kb upstream sequences of genes (or until the boundary of the previous gene if closer). We considered intergenic space, anything not belonging to these categories.…”

“…Genomic and bisulfite sequencing raw data are available on the ENA Sequence Read Archive (www.ebi.ac.uk/ena/) under study accession number PRJEB50950. Reference genome and annotations were previously published by Nunn et al (2022). From the annotation, we subset confident de novo gene annotations with an annotation edit distance score < 1.0 (source: T_arvense_v2).…”

“…Like A. thaliana, T. arvense is an annual and mostly selfing member of the Brassicaceae family, but it has a significantly larger genome of approx. 500Gb, which is richer in TEs and DNA methylation [36]. The species is an interesting study object also because it is currently being domesticated into a new biofuel and cover crop [37][38][39][40][41].…”

DNA methylation dynamics during stress response in woodland strawberry (Fragaria vesca)

“…It has long been established that DNA methylation is enriched in peri−/centromeric regions which follow the distribution of TEs over the chromosomes of genomes of the Brassicaceae family, as recently also confirmed for Thlaspi arvense [ 67 , 68 ]. In our study, while investigating the global distribution of DMRs over the F. vesca chromosomes, we found that regions with high DMR density correlated with regions enriched in Helitrons .…”