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

Autor:	Hoang NV; Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Walden N; Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany., Caracciolo L; Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands., Luoni SB; Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Retta M; Centre for Crop Systems Analysis, Wageningen University and Research, P.O. Box 430, 6700 AK Wageningen, The Netherlands., Li R; Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Wolters FC; Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.; Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Woldu T; Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Becker FFM; Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Verbaarschot P; Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Harbinson J; Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands., Driever SM; Centre for Crop Systems Analysis, Wageningen University and Research, P.O. Box 430, 6700 AK Wageningen, The Netherlands., Struik PC; Centre for Crop Systems Analysis, Wageningen University and Research, P.O. Box 430, 6700 AK Wageningen, The Netherlands., van Amerongen H; Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands., de Ridder D; Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Aarts MGM; Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands., Schranz ME; Biosystematics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Jazyk:	angličtina
Zdroj:	Annals of botany [Ann Bot] 2024 Oct 24. Date of Electronic Publication: 2024 Oct 24.
DOI:	10.1093/aob/mcae179
Abstrakt:	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. incana and R. sativus form a monophyletic clade in between the Brassica A/C and B genomes. We postulate that H. incana and R. sativus genomes are results of hybridization or introgression of the Brassica A/C and B genome types. Our results might explain the discrepancy observed in published studies regarding phylogenetic placement of H. incana and R. sativus in 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 in H. incana which likely facilitate its high-photosynthesis traits under high light. Conclusions: The improved H. incana genome assembly, annotation and results presented in this work will be a valuable resource for future research to unravel the genetic basis of its ability to maintain a high photosynthetic efficiency in high-light conditions and thereby improve photosynthesis for enhanced agricultural production. (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu