Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax

Abstract

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100–150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants.

Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

“…Seventy-three of the 115 PgZFP genes identified in this study were mapped to all 24 chromosomes of the Chinese ginseng 6 , with each chromosome having 1–6 PgZFP genes. Seventeen of 73 PgZFP genes mapped to the Chinese ginseng genome 6 were shown to be syntenic to 11 Arabidopsis orthologues in four of the five Arabidopsis chromosomes, Chromosomes 1, 3, 4, and 5, with each chromosome having 2–4 Arabidopsis orthologues (Fig. 1 A).…”

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Figure 1 The distribution of the PgZFP gene family in the ginseng genome and its family size variation among ginseng genotypes. ( A ) The positions of the PgZFP gene family in the Chinese ginseng genome 6 and its synteny with the Arabidopsis genome. The PgZFP genes were mapped to all 24 ginseng chromosomes indicated by light blue bars and their Arabidopsis orthologues were mapped to four of the five Arabidopsis chromosomes indicated by yellow bars.

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“…Database C is made of 48,211–79,134 unique transcripts per genotype. Moreover, three ginseng genome assemblies from three genotypes 4 – 6 were also used for this study.…”

“…We aligned the PgZFP genes identified above to three ginseng genome assemblies 4 – 6 using Blastn to determine their distribution in the ginseng genome 6 and the variation of the PgZFP gene family size among genotypes. The criteria of identity ≥ 99%, cover length ≥ 200 bp, and e-value ≤ 1.0E−100 were used for the alignment.…”

“…Kim et al 5 released the draft of the ginseng genome for another genotype, from which 59,352 genes were identified. Recently, Wang et al 6 reported a chromosome-sized assembly of the ginseng genome for the third genotype, from which 65,913 genes were identified. Wang et al 7 sequenced the transcriptome of a 4-year-old ginseng plant expressed in 14 tissues, assembled 248,992 transcript unigenes spliced from 130,557 gene models and quantified their expressions in the 14 tissues.…”