Expanding the Triangle of U: The genome assembly ofHirschfeldia incanaprovides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

Abstract

ABSTRACTThe Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific and interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event (Br-α, ∼15.9 million years ago), different lineages and species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention and loss (fractionation). Lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. The C3speciesHirschfeldia incanais studied as it displays high photosynthetic rates under high-light conditions. We present an improved chromosome-level genome assembly forH. incana(Nijmegen, v2.0) using nanopore and chromosome conformation capture (Hi-C) technologies, with 409Mb in size and an N50 of 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). The updated assembly and annotation allowed to investigate the WGT history ofH. incanain a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops.Hirschfeldia incana(x=7) shares extensive genome collinearity withRaphanus sativus(x=9). These two species share some commonalities withBrassica rapaandB. oleracea(A genome, x=10 and C genome, x=9, respectively) and other similarities withB. nigra(B genome, x=8). Phylogenetic analysis revealed thatH. incanaandR. sativusform a monophyletic clade in between theBrassicaA/C and B genomes. We postulate thatH. incanaandR. sativusgenomes are results of reciprocal hybridization combinations of theBrassicaA/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement ofH. incanaandR. sativusin relation to the “Triangle of U” species. Expression analysis of WGT retained gene copies revealed sub-genome expression divergence, likely due to neo- or sub-functionalization. Finally, we highlighted genes associated with physio-biochemical-anatomical adaptive changes observed inH. incanawhich likely facilitate its high-photosynthesis traits under high light.