Insights into the Superrosids Phylogeny and Flavonoid Synthesis from the Telomere-to-Telomere Gap-Free Genome Assembly of Penthorum chinense Pursh

Author:

Wang Zhoutao123,Zhou Junmei2,Pan Junjie2,Cheng Wei12,Fang Jie2,Lv Qundan2,Lin Xiaodan4,Cheng Wenliang2,Zhang Liangsheng1,Cheng Kejun253

Affiliation:

1. Zhejiang University Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, , Hangzhou 311300, China

2. Lishui Institute of Agriculture and Forestry Sciences Chemical Biology Center, , Lishui 323000, China

3. Zhejiang Kangning Pharmaceutical Co., Ltd , Lishui 323000, China

4. Zhejiang Shaowei Yuanzhi Science and Technology Development Co., Ltd , Lishui 323000, China

5. Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A&F University , Hangzhou, 311300, China

Abstract

Abstract The completion of the first telomere-to-telomere (T2T) genome assembly of Penthorum chinense Pursh (PC), a prominent medicinal plant in China, represents a significant achievement. This assembly spans a length of 257.5 Mb and consists of nine chromosomes. PC's notably smaller genome size in Saxifragales, compared to that of Paeonia ostii, can be attributed to the low abundance of transposable elements. By utilizing single-copy genes from thirty species, including twenty-eight other Superrosids species, we successfully resolved a previously debated Superrosids phylogeny. Our findings unveiled Saxifragales as the sister group to the core rosids, with both being the sister group to Vitales. Utilizing previously characterized cytochrome P450 (CYP) genes, we predicted the compound classes that most CYP genes of PC are involved in synthesizing, providing insight into PC's potential metabolic diversity. Metabolomic and transcriptomic data revealed that the richest sources of the three most noteworthy medicinal components in PC are young leaves and flowers. We also observed higher activity of upstream genes in the flavonoid synthesis pathway in these plant parts. Additionally, through weighted gene co-expression network analysis, we identified gene regulatory networks associated with the three medicinal components. Overall, these findings deepen our understanding of PC, opening new avenues for further research and exploration.

Publisher

Oxford University Press (OUP)

Subject

Horticulture,Plant Science,Genetics,Biochemistry,Biotechnology

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