The chromosome-level genome sequence and karyotypic evolution of
Megadenia pygmaea (Brassicaceae)
Abstract
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
pseudo-chromosomes. We annotated a total of 25,607 high-confidence
protein-coding genes and corroborated the phylogenetic affinity of
Megadenia with the expanded Lineage II, which contains 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 Brassicaceae Lineage II. However, an end-to-end
translocation between two ancestral chromosomes reduced the chromosome
number from n = 7 to n = 6, comparable to Megadenia. Our reference
genome provides fundamental information for use in horticulture, plant
breeding and evolutionary study of this genus.