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Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production

Chi Song, Fangfang Fu, Lulu Yang, Yan Niu, Zhaoyang Tian, Xiangxiang He, Xiaoming Yang, Jie Chen, Wei Sun, Tao Wan, et al.
(2021) COMMUNICATIONS BIOLOGY. 4(1).
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Abstract
Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.
Keywords
General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, Medicine (miscellaneous), MOLECULAR-CLONING, EARLY EVOLUTION, ANNOTATION, BIOSYNTHESIS, SEQUENCE, PLANTS, RATES

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MLA
Song, Chi, et al. “Taxus Yunnanensis Genome Offers Insights into Gymnosperm Phylogeny and Taxol Production.” COMMUNICATIONS BIOLOGY, vol. 4, no. 1, 2021, doi:10.1038/s42003-021-02697-8.
APA
Song, C., Fu, F., Yang, L., Niu, Y., Tian, Z., He, X., … Chen, S. (2021). Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production. COMMUNICATIONS BIOLOGY, 4(1). https://doi.org/10.1038/s42003-021-02697-8
Chicago author-date
Song, Chi, Fangfang Fu, Lulu Yang, Yan Niu, Zhaoyang Tian, Xiangxiang He, Xiaoming Yang, et al. 2021. “Taxus Yunnanensis Genome Offers Insights into Gymnosperm Phylogeny and Taxol Production.” COMMUNICATIONS BIOLOGY 4 (1). https://doi.org/10.1038/s42003-021-02697-8.
Chicago author-date (all authors)
Song, Chi, Fangfang Fu, Lulu Yang, Yan Niu, Zhaoyang Tian, Xiangxiang He, Xiaoming Yang, Jie Chen, Wei Sun, Tao Wan, Han Zhang, Yicheng Yang, Tian Xiao, Komivi Dossa, Xiangxiao Meng, Fuliang Cao, Yves Van de Peer, Guibin Wang, and Shilin Chen. 2021. “Taxus Yunnanensis Genome Offers Insights into Gymnosperm Phylogeny and Taxol Production.” COMMUNICATIONS BIOLOGY 4 (1). doi:10.1038/s42003-021-02697-8.
Vancouver
1.
Song C, Fu F, Yang L, Niu Y, Tian Z, He X, et al. Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production. COMMUNICATIONS BIOLOGY. 2021;4(1).
IEEE
[1]
C. Song et al., “Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production,” COMMUNICATIONS BIOLOGY, vol. 4, no. 1, 2021.
@article{8730948,
  abstract     = {{Taxol, a natural product derived from Taxus, is one of the most effective natural anticancer drugs and the biosynthetic pathway of Taxol is the basis of heterologous bio-production. Here, we report a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7 Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 Mb and 966.80 Mb, respectively. Phylogenomic analyses show that T. yunnanensis is most closely related to Sequoiadendron giganteum among the sampled taxa, with an estimated divergence time of 133.4-213.0 MYA. As with most gymnosperms, and unlike most angiosperms, there is no evidence of a recent whole-genome duplication in T. yunnanensis. Repetitive sequences, especially long terminal repeat retrotransposons, are prevalent in the T. yunnanensis genome, contributing to its large genome size. We further integrated genomic and transcriptomic data to unveil clusters of genes involved in Taxol synthesis, located on the chromosome 12, while gene families encoding hydroxylase in the Taxol pathway exhibited significant expansion. Our study contributes to the further elucidation of gymnosperm relationships and the Taxol biosynthetic pathway.}},
  articleno    = {{1203}},
  author       = {{Song, Chi and Fu, Fangfang and Yang, Lulu and Niu, Yan and Tian, Zhaoyang and He, Xiangxiang and Yang, Xiaoming and Chen, Jie and Sun, Wei and Wan, Tao and Zhang, Han and Yang, Yicheng and Xiao, Tian and Dossa, Komivi and Meng, Xiangxiao and Cao, Fuliang and Van de Peer, Yves and Wang, Guibin and Chen, Shilin}},
  issn         = {{2399-3642}},
  journal      = {{COMMUNICATIONS BIOLOGY}},
  keywords     = {{General Agricultural and Biological Sciences,General Biochemistry,Genetics and Molecular Biology,Medicine (miscellaneous),MOLECULAR-CLONING,EARLY EVOLUTION,ANNOTATION,BIOSYNTHESIS,SEQUENCE,PLANTS,RATES}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{8}},
  title        = {{Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production}},
  url          = {{http://dx.doi.org/10.1038/s42003-021-02697-8}},
  volume       = {{4}},
  year         = {{2021}},
}
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