Chromosome-scale assembly of the Kandelia obovata genome

Min Jie Hu, Wei Hong Sun, Wen Chieh Tsai, Shuang Xiang, Xing Kai Lai, De Qiang Chen, Xue Die Liu, Yi Fan Wang, Yi Xun Le, Si Ming Chen, Di Yang Zhang, Xia Yu, Wen Qi Hu, Zhuang Zhou, Yan Qiong Chen, Shuang Quan Zou, Zhong Jian Liu

Research output: Contribution to journalArticle

Abstract

The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.

Original languageEnglish
Article number75
JournalHorticulture Research
Volume7
Issue number1
DOIs
Publication statusPublished - 2020 Dec 1

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Genetics
  • Plant Science
  • Horticulture

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  • Cite this

    Hu, M. J., Sun, W. H., Tsai, W. C., Xiang, S., Lai, X. K., Chen, D. Q., Liu, X. D., Wang, Y. F., Le, Y. X., Chen, S. M., Zhang, D. Y., Yu, X., Hu, W. Q., Zhou, Z., Chen, Y. Q., Zou, S. Q., & Liu, Z. J. (2020). Chromosome-scale assembly of the Kandelia obovata genome. Horticulture Research, 7(1), [75]. https://doi.org/10.1038/s41438-020-0300-x