Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits

作者：Nam V. Hoang, Nora Walden, Ludovico Caracciolo, Sofía Bengoa Luoni, Moges Retta, Run Li, Felicia C Wolters, Tina Woldu, Frank Becker, Patrick Verbaarschot, Jeremy Harbinson, Steven M. Driever, P.C. Struik, Herbert van Amerongen, Dick de Ridder, Mark G. M. Aarts, M. Eric Schranz · 发表于：Annals of Botany · 年份：2024 · DOI：10.1093/aob/mcae179 · 被引用次数：4 · 研究领域：Genomics and Phylogenetic Studies、Photosynthetic Processes and Mechanisms、Chromosomal and Genetic Variations

BACKGROUND AND AIMS: The 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), differential lineage diversification and genomic changes contributed to an array of divergence in morphology, biochemistry, and physiology underlying photosynthesis-related traits. Here, the C3 species Hirschfeldia incana is studied as it displays high photosynthetic rates under high-light conditions. Our aim was to elucidate the evolution that gave rise to the genome of H. incana and its high-photosynthesis traits. METHODS: We reconstructed a chromosome-level genome assembly for H. 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 was subsequently employed to investigate the WGT history of H. incana in a comparative phylogenomic framework from the Brassiceae ancestral genomic blocks and related diploidized crops. KEY RESULTS: Hirschfeldia incana (x=7) shares extensive genome collinearity with Raphanus sativus (x=9). These two species share some commonalities with Brassica rapa and B. oleracea (A genome, x=10 and C genome, x=9, respectively) and other similarities with B. nigra (B genome, x=8). Phylogenetic analysis revealed that H. incan...