The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis

Yi Zuo; Hongbing Liu; Bin Li; Hang Zhao; Xiuli Li; Jiating Chen; Lu Wang; Qingbo Zheng; Yuqing He; Jiashuo Zhang; Minxian Wang; Chengzhi Liang; Lei Wang

doi:10.1016/j.celrep.2024.113909

The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis

Cell Rep. 2024 Mar 26;43(3):113909. doi: 10.1016/j.celrep.2024.113909. Epub 2024 Mar 6.

Authors

Yi Zuo¹, Hongbing Liu², Bin Li¹, Hang Zhao², Xiuli Li², Jiating Chen³, Lu Wang⁴, Qingbo Zheng¹, Yuqing He⁵, Jiashuo Zhang³, Minxian Wang⁶, Chengzhi Liang⁷, Lei Wang⁸

Affiliations

¹ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China.
² Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
³ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
⁴ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China.
⁵ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China.
⁶ CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
⁷ State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
⁸ Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wanglei@ibcas.ac.cn.

PMID: 38451814
DOI: 10.1016/j.celrep.2024.113909

Abstract

The deciduous tree Idesia polycarpa can provide premium edible oil with high polyunsaturated fatty acid contents. Here, we generate its high-quality reference genome, which is ∼1.21 Gb, comprising 21 pseudochromosomes and 42,086 protein-coding genes. Phylogenetic and genomic synteny analyses show that it diverged with Populus trichocarpa about 16.28 million years ago. Notably, most fatty acid biosynthesis genes are not only increased in number in its genome but are also highly expressed in the fruits. Moreover, we identify, through genome-wide association analysis and RNA sequencing, the I. polycarpa SUGAR TRANSPORTER 5 (IpSTP5) gene as a positive regulator of high oil accumulation in the fruits. Silencing of IpSTP5 by virus-induced gene silencing causes a significant reduction of oil content in the fruits, suggesting it has the potential to be used as a molecular marker to breed the high-oil-content cultivars. Our results collectively lay the foundation for breeding the elite cultivars of I. polycarpa.

Keywords: CP: Genomics; CP: Plants; I. polycarpa; IpSTP5; evolution; fatty acids; genome; oil biosynthesis.

MeSH terms

Base Sequence
Genome-Wide Association Study*
Phylogeny
Plant Breeding
Salicaceae* / genetics