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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 18, 2024

ABSTRACT The Brassiceae tribe encompasses many economically important crops and exhibits high intraspecific interspecific phenotypic variation. After a shared whole-genome triplication (WGT) event ( Br-α , ∼15.9 million years ago), different lineages species underwent differential chromosomal rearrangements (diploidization) leading to diverse patterns of gene retention loss (fractionation). Lineage diversification genomic changes contributed an array divergence in morphology, biochemistry, physiology underlying photosynthesis-related traits. C 3 Hirschfeldia incana is studied as it displays photosynthetic rates under high-light conditions. We present improved chromosome-level genome assembly for H. (Nijmegen, v2.0) using nanopore chromosome conformation capture (Hi-C) technologies, with 409Mb size N50 52Mb (a 10× improvement over the previously published scaffold-level v1.0 assembly). updated annotation allowed investigate WGT history comparative phylogenomic framework from ancestral blocks related diploidized crops. (x=7) shares extensive collinearity Raphanus sativus (x=9). These two share some commonalities Brassica rapa B. oleracea (A genome, x=10 x=9, respectively) other similarities nigra (B x=8). Phylogenetic analysis revealed that R. form monophyletic clade between A/C B genomes. postulate genomes are results reciprocal hybridization combinations types. Our might explain discrepancy observed studies regarding phylogenetic placement relation “Triangle U” species. Expression retained copies sub-genome expression divergence, likely due neo- or sub-functionalization. Finally, we highlighted genes associated physio-biochemical-anatomical adaptive which facilitate its high-photosynthesis traits light.

Language: Английский

Blazing a trail towards higher photosynthetic efficiency : A multi-dimensional study of Hirschfeldia incana

Published: Jan. 1, 2023

Improving C 3 photosynthesis by exploiting natural genetic variation: Hirschfeldia incana as a model species The genome sequence of incana, new Brassicaceae to improve photosynthetic light-use efficiency 4 Comparative transcriptomics and relatives highlights differences in pathways 5 Analysis variation panel 6 General discussion

Language: Английский