The Larix kaempferi genome reveals new insights into wood properties

• Published in: Journal of integrative plant biology Vol. 64; no. 7; pp. 1364 - 1373
• Main Authors: Sun, Chao, Xie, Yun‐Hui, Li, Zhen, Liu, Yan‐Jing, Sun, Xiao‐Mei, Li, Jing‐Jing, Quan, Wei‐Peng, Zeng, Qing‐Yin, Van de Peer, Yves, Zhang, Shou‐Gong
• Format: Journal Article
• Language: English
• Published: China (Republic : 1949- ) Wiley Subscription Services, Inc 01.07.2022; VIB Center for Plant Systems Biology,Ghent B-9052,Belgium; Department of Biochemistry,Genetics and Microbiology,Pretoria,South Africa; State Key Laboratory of Tree Genetics and Breeding,Chinese Academy of Forestry,Beijing 100091,China; 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%Department of Plant Biotechnology and Bioinformatics,Ghent University,Gent B-9052,Belgium; VIB Center for Plant Systems Biology,Ghent B-9052,Belgium%State Key Laboratory of Tree Genetics and Breeding,Chinese Academy of Forestry,Beijing 100091,China%Nextomics Biosciences Co.,Ltd,Wuhan 430073,China%Department of Plant Biotechnology and Bioinformatics,Ghent University,Gent B-9052,Belgium
• Subjects: afforestation; Biological evolution; Coniferous trees; Conifers; evolution; Evolution & development; evolutionary adaptation; Gene expression; Gene regulation; Genes; genome; Genomes; Larix kaempferi; Lignin; lignin content; Long terminal repeat; Nucleotide sequence; plant biology; polymerization; retrotransposons; terminal repeat sequences; transcription (genetics); Transcriptomes; transcriptomics; Wood; wood properties; genome; evolution; Larix kaempferi; gene expression; wood properties
• ISSN: 1672-9072; 1744-7909; 1744-7909
• DOI: 10.1111/jipb.13265

ABSTRACT 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. Examination of the high‐quality genome of the Japanese larch Larix kaempferi reveals key features of this tree species and illustrates the crucial roles of genes encoding laccase and Class III peroxidases in wood properties of conifers.