J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (7): 1364-1373.DOI: 10.1111/jipb.13265

• Functional Omics and Systems Biology • Previous Articles     Next Articles

The Larix kaempferi genome reveals new insights into wood properties

Chao Sun1,2†, Yun‐Hui Xie1,2†, Zhen Li3,4†, Yan‐Jing Liu1, Xiao‐Mei Sun1,2, Jing‐Jing Li5, Wei‐Peng Quan5, Qing‐Yin Zeng1*, Yves Van de Peer3,4,6* and Shou‐Gong Zhang1,2*   

  1. 1 State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
    2 Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
    3 Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent B‐9052, Belgium
    4 VIB Center for Plant Systems Biology, Ghent B‐9052, Belgium
    5 Nextomics Biosciences Co., Ltd, Wuhan 430073, China
    6 Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa

    These authors contributed equally to this work.
    *Correspondences: Qing‐Yin Zeng (qingyin.zeng@caf.ac.cn); Yves Van de Peer (yves.vandepeer@psb.vib-ugent.be); Shou‐Gong Zhang (sgzhang@caf.ac.cn, Dr. Zhang is fully responsible for the distributions of all materials associated with this article)
  • Received:2022-03-10 Accepted:2022-04-18 Online:2022-04-20 Published:2022-07-01


Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

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