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Science China. Life sciences
03, 2022;65 (3): 515-528.

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

Tao Lin, Xia Xu, Huilong Du, Xiuli Fan, Qingwen Chen, Chunyan Hai, Zijian Zhou, Xiao Su, Liquan Kou, Qiang Gao, Lingwei Deng, Jinsheng Jiang, Hanli You, Yihua Ma, Zhukuan Cheng, Guodong Wang, Chengzhi Liang, Guomin Zhang, Hong Yu, Jiayang Li
Author Information
  1. Tao Lin: 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.
  2. Xia Xu: 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.
  3. Huilong Du: 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.
  4. Xiuli Fan: 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.
  5. Qingwen Chen: 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.
  6. Chunyan Hai: 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.
  7. Zijian Zhou: State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
  8. Xiao Su: State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.
  9. Liquan Kou: 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.
  10. Qiang Gao: Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
  11. Lingwei Deng: Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
  12. Jinsheng Jiang: Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
  13. Hanli You: 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.
  14. Yihua Ma: 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.
  15. Zhukuan Cheng: 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.
  16. Guodong Wang: 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.
  17. Chengzhi Liang: 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. cliang@genetics.ac.cn.
  18. Guomin Zhang: Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China. zgm_2290@163.com.
  19. Hong Yu: 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. hyu@genetics.ac.cn.
  20. Jiayang Li: 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.
PMID: 34939160 DOI: 10.1007/s11427-021-2033-2

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.

Keywords

Taraxacum kok-saghyz Taraxacum mongolicum comparative genomics natural rubber biosynthesis pathway reference genome

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MeSH Term

Biosynthetic Pathways
DNA Transposable Elements
Genome, Plant
Rubber
Taraxacum

Chemicals

DNA Transposable Elements
Rubber
Journal Article

Links to CNCB-NGDC Resources

BioProject: PRJCA000437 (Genomic sequence of Taraxacum kok-saghyz Rodin)
BioProject: PRJCA005187 (Taraxacum reference genomes)
GSA: CRA003851 (Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis)
GSA: CRA010603 (Raw sequencing data for genome assembly of Taraxacum kok-saghyz Rodin)
GSA: CRA004216 (Raw sequencing data for genome assembly and annotation of Taraxacum reference genome)
GWH: GWHBCHF00000000 (Taraxacum kok-saghyz)
GWH: GWHBCHG00000000 (Taraxacum mongolicum)

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