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Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum

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Abstract

Plants belonging to the genus Taraxacum are widespread all over the world, which contain rubber-producing and non-rubber-producing species. However, the genomic basis underlying natural rubber (NR) biosynthesis still needs more investigation. Here, we presented high-quality genome assemblies of rubber-producing T. kok-saghyz TK1151 and non-rubber-producing T. mongolicum TM5. Comparative analyses uncovered a large number of genetic variations, including inversions, translocations, presence/absence variations, as well as considerable protein divergences between the two species. Two gene duplication events were found in these two Taraxacum species, including one common ancestral whole-genome triplication and one subsequent round of gene amplification. In genomes of both TK1151 and TM5, we identified the genes encoding for each step in the NR biosynthesis pathway and found that the SRPP and CPT gene families have experienced a more obvious expansion in TK1151 compared to TM5. This study will have large-ranging implications for the mechanism of NR biosynthesis and genetic improvement of NR-producing crops.

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Data availability

Raw sequencing data for genome assembly and annotation have been deposited into the Genome Sequence Archive (GSA) database in BIG Data Center under Accession Number PRJCA005187 and PRJCA000437. The final genome assemblies of TK1151 and TM5 were deposited into the Genome Warehouse (GWH) database in the BIG Data Center under Accession Number GWHBCHF00000000 and GWHBCHG00000000, respectively.

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Acknowledgements

This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA24030504 and XDA24040305), the National Natural Science Foundation of China (32000144), and the Key Research Program of the Chinese Academy of Sciences (ZDRW-ZS-2018-2). We thank Ms. Fengqin Dong (Institute of Botany, Chinese Academy of Sciences) and Mr. Yanbao Tian (National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences) for assistance in transmission electron microscopy analysis.

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  1. Contributed equally to this work

Authors and Affiliations

  1. State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China

    Tao Lin, Xia Xu, Huilong Du, Xiuli Fan, Qingwen Chen, Chunyan Hai, Liquan Kou, Hanli You, Yihua Ma, Zhukuan Cheng, Guodong Wang, Chengzhi Liang, Hong Yu & Jiayang Li

  2. State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China

    Tao Lin, Zijian Zhou & Xiao Su

  3. University of Chinese Academy of Sciences, Beijing, 100049, China

    Xiuli Fan, Qingwen Chen, Chunyan Hai, Hanli You, Yihua Ma, Chengzhi Liang & Jiayang Li

  4. Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Qiang Gao

  5. Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China

    Lingwei Deng, Jinsheng Jiang & Guomin Zhang

  6. Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, 510642, China

    Jiayang Li

  7. School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China

    Huilong Du

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  1. Tao Lin
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  2. Xia Xu
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Correspondence to Chengzhi Liang, Guomin Zhang or Hong Yu.

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Lin, T., Xu, X., Du, H. et al. Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum. Sci. China Life Sci. 65, 515–528 (2022). https://doi.org/10.1007/s11427-021-2033-2

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