Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana

Matthiola incana, commonly known as stock and gillyflower, is a widely grown ornamental plant whose genome is significantly larger than that of other species in the mustard family. However, the evolutionary history behind such a large genome (~2 Gb) is still unknown. Here, we have succeeded in obtaining a high-quality chromosome-scale genome assembly of M. incana by integrating PacBio HiFi reads, Illumina short reads and Hi-C data. The resulting genome consists of seven pseudochromosomes with a length of 1965 Mb and 38 245 gene models. Phylogenetic analysis indicates that M. incana and other taxa of the supertribe Hesperodae represent an early-diverging lineage in the evolutionary history of the Brassicaceae. Through a comparative analysis, we revisited the ancestral Hesperodae karyotype (AHK, n = 7) and found several differences from the well-established ancestral crucifer karyotype (ACK, n = 8) model, including extensive inter- and intra-chromosomal rearrangements. Our results suggest that the primary reason for genome obesity in M. incana is the massive expansion of long terminal repeat retrotransposons (LTR-RTs), particularly from the Angela, Athila and Retand families. CHG methylation modification is obviously reduced in the regions where the highest density of Copia-type LTR-RTs and the lowest density of Gypsy-type LTR-RTs overlap, corresponding to the putative centromeres. Based on insertion times and methylation profiling, recently inserted LTR-RTs were found to have a significantly different methylation pattern compared to older ones.

紫罗兰（Matthiola incana），通常俗称stock与gillyflower，是一种广泛栽培的观赏植物，其基因组尺寸显著大于十字花科（Brassicaceae）其他物种。然而，这一约2 Gb的庞大基因组的演化起源仍未明确。本研究通过整合PacBio HiFi测序读长、Illumina短读长测序数据与Hi-C交互数据，成功获得了高质量的紫罗兰染色体级基因组组装结果。该组装基因组包含7条假染色体，总长度为1965 Mb，共注释得到38245个基因模型。系统发育分析显示，紫罗兰（M. incana）与香花芥超族（supertribe Hesperodae）的其他类群共同构成了十字花科演化历史中的一个早期分化支系。通过比较基因组分析，我们重新解析了祖先香花芥超族核型（AHK, n=7），并发现其与已被广泛认可的祖先十字花科核型（ACK, n=8）模型存在多处差异，包括广泛的染色体间及染色体内重排事件。本研究结果表明，紫罗兰基因组膨大的主要原因是长末端重复序列逆转录转座子（long terminal repeat retrotransposons, LTR-RTs）的大规模扩增，尤其是来自Angela、Athila及Retand家族的转座子。在Copia型LTR-RTs密度最高且Gypsy型LTR-RTs密度最低的重叠区域——即推定的着丝粒区域——CHG甲基化修饰水平显著降低。通过插入时间分析与甲基化谱分析，我们发现新近插入的LTR-RTs与古老转座子的甲基化模式存在显著差异。