Sang-Ho Kang^1,11,*, Ramesh Prasad Pandey^2,9,11, Chang-Muk Lee³, Joon-Soo Sim³, Jin-Tae Jeong⁴, Beom-Soon Choi⁵, Myunghee Jung⁶, Daniel Ginzburg⁷, Kangmei Zhao⁷, So Youn Won¹, Tae-Jin Oh2, Yeisoo Yu^5,10, Nam-Hoon Kim⁵, Ok Ran Lee⁸, Tae-Ho Lee¹, Puspalata Bashyal², Tae-Su Kim², Woo-Haeng Lee², Charles Hawkins⁷, Chang-Kug Kim¹, Jung Sun Kim¹, Byoung Ohg Ahn¹, Seung Yon Rhee^7,* & Jae Kyung Sohng^2,*

¹Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea.
²Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan 31460, Republic of Korea.
³Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Republic of Korea.
⁴Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, RDA, Eumseong 55365, Republic of Korea.
⁵Phyzen Genomics Institute, Seongnam 13488, Republic of Korea.
⁶Department of Forest Science, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Republic of Korea.
⁷Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA. ⁸Department of Applied Plant Science, College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Republic of Korea.
⁹Present address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
¹⁰Present address: DNACARE Co. Ltd, Seoul 06730, Republic of Korea.

¹¹These authors contributed equally: Sang-Ho Kang, Ramesh Prasad Pandey.

^*Corresponding author

Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.