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.

中文翻译：

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染色体水平的 Thlaspi arvense 基因组为转化研究和寒冷气候下新驯化的经济覆盖作物提供了新工具

蝾螈(field pennycress) 被驯化为一种冬季一年生油料作物，能够在不增加土地使用的情况下改善生态系统并提高农业生产力。它是一种生命周期短的自交二倍体，易于遗传操作，使其成为遗传学和表观遗传学的可利用的基于田间的模型物种。高质量参考基因组的可用性对于理解仙人掌生理学和阐明其在十字花科内的进化历史至关重要。在这里，我们提出了 var 的染色体水平基因组组装。MN106-Ref 具有改进的基因注释，并使用它来研究高度适合遗传转化的两个种质（MN108 和 Spring32-10）之间的基因结构差异。我们描述了非编码 RNA、假基因和转座因子，并突出组织特异性表达和甲基化模式。对 40 个野生种质的重新测序提供了对全基因组遗传变异的见解，并确定了幼苗颜色表型的 QTL 区域。总而言之，这些数据将作为一种工具，用于一般的竹芋改良和十字花科的转化研究。