Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.

入侵性日本莠竹（Microstegium vimineum）可侵染多种生态系统，并对美国东部地区的生物多样性构成严重威胁。然而，目前学界对其入侵种群中快速适应、表型可塑性及表观遗传调控的潜在分子机制仍知之甚少。本研究报道了日本莠竹的染色体级基因组组装结果，以解析其基因组动态、演化历程、适应性机制以及表型可塑性的基因组学基础。研究采用PacBio与Dovetail Genomics Omni-C测序相结合的从头组装策略，构建了总长度为1.12 Gb的基因组，其支架N50（scaffold N50）长度达53.44 Mb。该组装包含23条假染色体，覆盖了99.96%的基因组序列。通用单拷贝同源基因集评估（BUSCO）结果显示，该组装覆盖了80.3%的禾本目（Poales）基因家族。预测该基因组共编码39604个蛋白质编码基因，其中26288个获得了功能注释。此外，该基因组中重复序列占比达66.68%，其中以未分类重复序列（35.63%）和长末端重复（long terminal repeat, LTR）反转录转座子（26.90%）为主。与其他禾本科植物类似，Gypsy家族（41.07%）与Copia家族（32%）是丰度最高的两类LTR反转录转座子家族。绝大多数LTR反转录转座子在过去100万至200万年间发生了显著扩张，提示存在较为年轻的LTR反转录转座子谱系。通过Ks位点分析（Ks plots），我们发现了日本莠竹特有的全基因组复制事件，该事件区别于更为古老的禾本科特异性复制事件。日本莠竹的基因组组装与注释结果将成为一项重要的基因组学资源，可为入侵过程研究、禾本科植物多倍化的历史与后果分析提供支撑，同时也为自然资源管理者提供了关键的研究工具。