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.