Sophora genomes provide insight into the evolution of alkaloid metabolites along with small-scale gene duplication

BMC Genomics

Research

Halim Park¹  Yejin Lee¹  Sanghwa Yoon¹  Yang Jae Kang²  Myounghai Kwak³ 

[1] Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 52828, Jinju, Republic of Korea;Division of Bio & Medical Bigdata Department (BK4 Program), Gyeongsang National University, 52828, Jinju, Republic of Korea;Division of Life Science Department, Gyeongsang National University, Jinju, Republic of Korea;National Institute of Biological Resources, 22689, Incheon, Republic of Korea;

关键词: Congeneric;    Divergence;    Evolution;    Functional annotation;    Genome;    Phylogeny;    Secondary metabolite;    Small-scale duplication;    Sophora;   

DOI  :  10.1186/s12864-023-09516-w

 received in 2022-12-30, accepted in 2023-07-13,  发布年份 2023

来源: Springer

【 摘 要 】

The genus Sophora (Fabaceae) includes medicinal plants that have been used in East Asian countries since antiquity. Sophora flavescens is a perennial herb indigenous to China, India, Japan, Korea, and Russia. Its dried roots have antioxidant, anti-inflammatory, antibacterial, apoptosis-modulating, and antitumor efficacy. The congeneric S. koreensis is endemic to Korea and its genome is less than half the size of that of S. flavescens. Nevertheless, this discrepancy can be used to assemble and validate the S. flavescens genome. A comparative genomic study of the two genomes can disclose the recent evolutionary divergence of the polymorphic phenotypic profiles of these species. Here, we used the PacBio sequencing platform to sequence and assemble the S. koreensis and S. flavescens genomes. We inferred that it was mainly small-scale duplication that occurred in S. flavescens. A KEGG analysis revealed pathways that might regulate the pharmacologically important secondary metabolites in S. flavescens and S. koreensis. The genome assemblies of Sophora spp. could be used in comparative genomics and data mining for various plant natural products.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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