Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome-level reference genome for the family Meliaceae

Yun-Tao Ji, Zhihui Xiu, Chun-Hai Chen, Youru Wang, Jing-Xia Yang, Juan-Juan Sui, San-Jie Jiang, Ping Wang, Shao-Yun Yue, Qian-Qian Zhang, Ji-Liang Jin, Guo-Shu Wang, Qian-Qian Wei, Bing Wei, Juan Wang, Hai-Lin Zhang, Qiu-Yan Zhang, Jun Liu*, Chang-Jin Liu*, Jian-Bo Jian*Chang-Qing Qu*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high-quality hardwood. However, the absence of a reference genome has hindered in-depth molecular and evolutionary studies of this plant. In this study, we report a high-quality T. sinensis genome assembly, with scaffolds anchored to 28 chromosomes and a total assembled length of 596 Mb (contig N50 = 1.5 Mb and scaffold N50 = 21.5 Mb). A total of 34,345 genes were predicted in the genome after homology-based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1-103.1 million years ago, and the T. sinensis genome underwent a recent genome-wide duplication event at ~7.8 million years and one more ancient whole genome duplication event at ~71.5 million years. These results provide a high-quality chromosome-level reference genome for T. sinensis and confirm its evolutionary position at the genomic level. Such information will offer genomic resources to study the molecular mechanism of terpenoid biosynthesis and the formation of flavour compounds, which will further facilitate its molecular breeding. As the first chromosome-level genome assembled in the family Meliaceae, it will provide unique insights into the evolution of members of the Meliaceae.
Original languageEnglish
JournalMolecular Ecology Resources
Issue number4
Pages (from-to)1243-1255
Number of pages13
Publication statusPublished - 2021


  • Evolution
  • Hi-C
  • Nanopore
  • Toona sinensis
  • Whole genome duplication


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