Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Yanting Shen (), Wanying Li, Ying Zeng, Zhipeng Li, Yiqiong Chen, Jixiang Zhang, Hong Zhao, Lingfang Feng, Dongming Ma, Xiaolu Mo, Puyue Ouyang, Lili Huang, Zheng Wang, Yuannian Jiao and Hong-bin Wang ()
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Yanting Shen: Guangzhou University of Chinese Medicine
Wanying Li: Guangzhou University of Chinese Medicine
Ying Zeng: Guangzhou University of Chinese Medicine
Zhipeng Li: Guangzhou University of Chinese Medicine
Yiqiong Chen: Guangzhou University of Chinese Medicine
Jixiang Zhang: Chinese Academy of Sciences
Hong Zhao: Beijing Academy of Agriculture and Forestry Sciences
Lingfang Feng: Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education
Dongming Ma: Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education
Xiaolu Mo: Guangdong Food and Drug Vocational College
Puyue Ouyang: Guangdong Food and Drug Vocational College
Lili Huang: Guangzhou University of Chinese Medicine
Zheng Wang: Beijing Academy of Agriculture and Forestry Sciences
Yuannian Jiao: Chinese Academy of Sciences
Hong-bin Wang: Guangzhou University of Chinese Medicine

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family, is an important aromatic plant that has been widely used in medicine and perfumery. Here, we report a 1.94 Gb chromosome-scale assembly of the patchouli genome (contig N50 = 7.97 Mb). The gene annotation reveals that tandem duplication of sesquiterpene biosynthetic genes may be a major contributor to the biosynthesis of patchouli bioactivity components. We further phase the genome into two distinct subgenomes (A and B), and identify a chromosome substitution event that have occurred between them. Further investigations show that a burst of universal LTR-RTs in the A subgenome lead to the divergence between two subgenomes. However, no significant subgenome dominance is detected. Finally, we track the evolutionary scenario of patchouli including whole genome tetraploidization, subgenome divergency, hybridization, and chromosome substitution, which are the key forces to determine the complexity of patchouli genome. Our work sheds light on the evolutionary history of patchouli and offers unprecedented genomic resources for fundamental patchouli research and elite germplasm development.

Date: 2022
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DOI: 10.1038/s41467-022-31121-w

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