Introduction
Karyotypic changes in chromosome number and structure, in addition to polyploidy, are critical drivers in the divergent evolution of diverse plant species and lineages (Stebbins, 1971). Karyotypic changes comprise both chromosome number and large-scale structure, which can independently, or in combination, promote evolutionary divergence (Arnegard et al., 2014). The rapid diversification of Brassicaeae arose not only by polyploidy, but through karyotypic changes, providing a useful model system to study the diverse forms of karyotypic evolution (Lysak et al., 2016; Mandáková & Lysak, 2008). The Brassicaeae are a large family comprised of ca. 350 genera and nearly 4,000 species of angiosperm (Kiefer et al., 2014), including scientifically and commercially important species like Arabidopsis thaliana , vegetable or oil crops of Brassica or Raphanus , spices (Armoracia and Eutrema ) and ornamentals (Arabis ,Hesperis , Lobularia and Matthiola ) (Nikolov et al., 2019). Three major Lineages (I, II, and III) or six major clades were identified within the core Brassicaceae (Beilstein et al., 2008; Guo et al., 2017; Huang et al., 2016; Nikolov et al., 2019). The model species A. thaliana is included in the Lineage I, while the Lineage II contains agricultural crops, such as Brassica napus , Brassica rapaand Raphanus sativus (Lv et al., 2020; Nikolov et al., 2019). The number of chromosomes can vary greatly between Lineage I and II (Lysak, 2014). Comparative genomics and chromosome painting revealed that the ancestral karyotype of the Lineage I, the Ancestral Crucifer Karyotype (ACK), was comprised of eight chromosomes (n = 8) and 22 genomic blocks (GBs) (Lysak et al., 2016). The inferred ancestral karyotype of the Lineage II, the ‘Proto-Calepineae Karyotype’ (PCK, n = 7; Mandáková et al., 2018; Mandáková & Lysak, 2008), was found to be derived from the ancestral PCK (ancPCK, n = 8) through descending dysploidy, namely a reduction in chromosome number (Geiser et al., n.d.; Mandáková et al., 2018).
Megadenia is a genus of Brassicaeae with a chromosome number 2n = 12 and relatively few described species, disjunctly distributed across the Qinghai-Tibet Plateau, in northern China, to Asian Russia, and growing at elevation ranges from 400 to 4000 m a.s.l. (Artyukova et al., 2014; Dorofeyev, 2004; German & Al-Shehbaz, 2008; Zhou, 2001). All species ofMegadenia are confined to shady habitats, growing under shrubs and trees or in caves, and have the potential to be horticulturally valuable shade-loving plants (Artyukova et al., 2014). Recent phylogenetic analysis indicates the early divergence of Megadeniafrom other members of the Lineage II (Guo et al., 2017). This study aimed to understand the structure and chromosome evolution of theM. pygmaea nuclear genome. This research established the detailed chromosome structure and performed a comparative analysis to closely related Brassicaceae to inform understanding of the PCK genome using a chromosome-level de novogenome assembly and chromosome painting analysis. We highlighted the potential mechanism underlying the origin of the six Megadeniachromosomes and revealed that an end-to-end chromosome translocation likely mediated the reduction of chromosomes from the PCK-like genome (n = 7) to the extant Megadenia genome (n = 6). The new reference genome of M. pygmaea provides information for advancing the horticultural use of Megadenia and aids future investigations into evolutions and uniquely disjunct biogeography of this genus.