The Cardamine enshiensis genome reveals whole genome duplication

Cardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited. Here, we report a chromosome-level genome assembly of C. enshiensis, which consists of 443.4 Mb in 16 chromosomes with a scaffold N50 of 24 Mb. To elucidate the mechanism of Se tolerance and hyperaccumulation in C. enshiensis, we generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes. The results reveal that flavonoid, glutathione, and lignin biosynthetic pathways may play important roles in protecting C. enshiensis from stress induced by Se. Hi-C analysis of chromatin interaction patterns showed that the chromatin of C. enshiensis is partitioned into A and B compartments, and strong interactions between the two telomeres of each chromosome were correlated with histone modifications, epigenetic markers, DNA methylation, and RNA abundance.

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Fig: Genomic features and WGD in C. enshiensis: a Characteristics of the 16 chromosomes of C. enshiensis with a window size of 200 kb. The displayed plots are the gene density, repeated density, GC density, RNA, and relationships between syntenic blocks. b Synonymous substitution rate (Ks) distributions of syntenic blocks for C. hirsuta paralogs and orthologs. cCircos plots showing synteny between the genomes of C. hirsuta and C. enshiensis. d Inferred phylogenetic tree constructed with orthologs across 9 species, including their divergence times and WGDs. The posterior probabilities for all branches exceeded 0.99. α and β: the ancient α and β WGDs occurred about 47 and 124 million years ago.

Se supplementation could affect the 3D chromatin architecture of C. enshiensis at the compartment level. Genes with compartment changes after Se treatment were involved in selenocompound metabolism, and genes in regions with topologically associated domain insulation participated in cellular responses to Se, Se binding, and flavonoid biosynthesis. This multiomics research provides molecular insight into the mechanism underlying Se tolerance and hyperaccumulation in C. enshiensis.

Huang, C., Ying, H., Yang, X. et al. The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance. Cell Discov 7, 62 (2021). https://doi.org/10.1038/s41421-021-00286-x

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