Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high‐quality chromosome‐scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high‐throughput chromosome conformation capture (Hi‐C). The assembled genome is 215.2 Mb and is anchored on six pseudochromosomes. We annotated a total of 25,607 high‐confidence protein‐coding genes and corroborated the phylogenetic affinity of Megadenia with the Brassicaceae expanded lineage II, containing numerous agricultural crops. We dated the divergence of Megadenia from its closest relatives to 27.04 (19.11–36.60) million years ago. A reconstruction of the chromosomal composition of the species was performed based on the de novo assembled genome and comparative chromosome painting analysis. The karyotype structure of M. pygmaea is very similar to the previously inferred proto‐Calepineae karyotype (PCK; n = 7) of the lineage II. However, an end‐to‐end translocation between two ancestral chromosomes reduced the chromosome number from n = 7 to n = 6 in Megadenia. Our reference genome provides fundamental information for karyotypic evolution and evolutionary study of this genus.

中文翻译：

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Megadenia pygmaea (Brassicaceae) 染色体水平的基因组序列和核型进化

染色体数量和结构的核型变化是不同植物物种和谱系分化进化的驱动因素。本研究旨在揭示巨株属（十字花科）独特核型（2n = 12）的起源和系统发育关系。使用纳米孔长读长和高通量染色体构象捕获 (Hi-C)为Megadenia pygmaea组装了高质量的染色体规模基因组。组装的基因组为 215.2 Mb，并锚定在六个假染色体上。我们共注释了 25,607 个高置信度蛋白质编码基因，并证实了Megadenia与包含大量农作物的十字花科扩展谱系 II的系统发育亲和性。我们约会了Megadenia的分歧从它的近亲到 27.04 (19.11-36.60) 万年前。基于新组装的基因组和比较染色体染色分析，对该物种的染色体组成进行了重建。M. pygmaea的核型结构与先前推断 的谱系 II 的原始 Calepineae 核型 (PCK; n = 7)非常相似。然而，两条祖先染色体之间的端到端易位使Megadenia 中的染色体数量从n  = 7 减少到n  = 6 。我们的参考基因组为该属的核型进化和进化研究提供了基本信息。