Genome assembly of the milky mangrove Excoecaria agallocha

Hong Kong Biodiversity Genomics Consortium

doi:10.46471/gigabyte.119

Genome assembly of the milky mangrove Excoecaria agallocha

GigaByte. 2024 Apr 25:2024:gigabyte119. doi: 10.46471/gigabyte.119. eCollection 2024.

Author

Hong Kong Biodiversity Genomics Consortium

Collaborators

Hong Kong Biodiversity Genomics Consortium:
Jerome H L Hui¹, Ting Fung Chan², Leo Lai Chan³, Siu Gin Cheung⁴, Chi Chiu Cheang^{5

6}, James Kar-Hei Fang⁷, Juan Diego Gaitan-Espitia⁸, Stanley Chun Kwan Lau⁹, Yik Hei Sung^{10

11}, Chris Kong Chu Wong¹², Kevin Yuk-Lap Yip^{13

14}, Yingying Wei¹⁵, Sean Tsz Sum Law¹, Wai Lok So¹, Wenyan Nong¹, David Tai Wai Lau¹⁶, Shing Yip Lee¹⁷, Ho Yin Yip¹

Affiliations

¹ School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China.
² School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.
³ State Key Laboratory of Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.
⁴ State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China.
⁵ Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong SAR, China.
⁶ EcoEdu PEI, Charlottetown, PE, C1A 4B7, Canada.
⁷ Department of Food Science and Nutrition, Research Institute for Future Food, and State Key Laboratory of Marine Pollution, The Hong Kong Polytechnic University, Hong Kong SAR, China.
⁸ The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China.
⁹ Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
¹⁰ Science Unit, Lingnan University, Hong Kong SAR, China.
¹¹ School of Allied Health Sciences, University of Suffolk, Ipswich, IP4 1QJ, UK.
¹² Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China.
¹³ Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
¹⁴ Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
¹⁵ Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China.
¹⁶ Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
¹⁷ Simon F.S. Li Marine Science Laboratory, The Chinese University of Hong Kong, Hong Kong SAR, China.

Abstract

The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4%, with 86.08% of sequences anchored to 18 pseudomolecules. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.

Grants and funding

This work was funded and supported by the Hong Kong Research Grant Council Collaborative Research Fund (C4015-20EF), CUHK Strategic Seed Funding for Collaborative Research Scheme (3133356) and CUHK Group Research Scheme (3110154).