Genome assembly of the milky mangrove Excoecaria agallocha

Jerome H.L. Hui; Ting Fung Chan; Leo Lai Chan; Siu Gin Cheung; Chi Chiu Cheang; James Kar Hei Fang; Juan Diego Gaitan-Espitia; Stanley Chun Kwan Lau; Yik Hei Sung; Chris Kong Chu Wong; Kevin Yuk Lap Yip; Yingying Wei; Sean Tsz Sum Law; Wai Lok So; Wenyan Nong; David Tai Wai Lau; Shing Yip Lee; Ho Yin Yip; Hong Kong Biodiversity Genomics Consortium

doi:10.46471/gigabyte.119

Genome assembly of the milky mangrove Excoecaria agallocha

Jerome H.L. Hui^*, Ting Fung Chan, Leo Lai Chan, Siu Gin Cheung, Chi Chiu Cheang, James Kar Hei Fang, Juan Diego Gaitan-Espitia, Stanley Chun Kwan Lau, Yik Hei Sung, Chris Kong Chu Wong, Kevin Yuk Lap Yip, Yingying Wei, Sean Tsz Sum Law, Wai Lok So, Wenyan Nong, David Tai Wai Lau, Shing Yip Lee, Ho Yin Yip, Hong Kong Biodiversity Genomics Consortium

^*Corresponding author for this work

Department of Biology

Research output: Contribution to journal › Journal article › peer-review

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.

Original language	English
Number of pages	10
Journal	GigaByte
Volume	2024
DOIs	https://doi.org/10.46471/gigabyte.119
Publication status	Published - 25 Apr 2024

Scopus Subject Areas

Biochemistry, Genetics and Molecular Biology (miscellaneous)
Biotechnology
Genetics
Molecular Medicine

User-Defined Keywords

Botany
Genetics and Genomics
Plant Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.46471/gigabyte.119Licence: CC BY

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Hui, J. H. L., Chan, T. F., Chan, L. L., Cheung, S. G., Cheang, C. C., Fang, J. K. H., Gaitan-Espitia, J. D., Lau, S. C. K., Sung, Y. H., Wong, C. K. C., Yip, K. Y. L., Wei, Y., Law, S. T. S., So, W. L., Nong, W., Lau, D. T. W., Lee, S. Y., Yip, H. Y., & Hong Kong Biodiversity Genomics Consortium (2024). Genome assembly of the milky mangrove Excoecaria agallocha. GigaByte, 2024. https://doi.org/10.46471/gigabyte.119

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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.",

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AU - Hui, Jerome H.L.

AU - Chan, Ting Fung

AU - Chan, Leo Lai

AU - Cheung, Siu Gin

AU - Cheang, Chi Chiu

AU - Fang, James Kar Hei

AU - Gaitan-Espitia, Juan Diego

AU - Lau, Stanley Chun Kwan

AU - Sung, Yik Hei

AU - Wong, Chris Kong Chu

AU - Yip, Kevin Yuk Lap

AU - Wei, Yingying

AU - Law, Sean Tsz Sum

AU - So, Wai Lok

AU - Nong, Wenyan

AU - Lau, David Tai Wai

AU - Lee, Shing Yip

AU - Yip, Ho Yin

AU - Hong Kong Biodiversity Genomics Consortium

PY - 2024/4/25

Y1 - 2024/4/25

N2 - 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.

AB - 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.

KW - Botany

KW - Genetics and Genomics

KW - Plant Genetics

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DO - 10.46471/gigabyte.119

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VL - 2024

JO - GigaByte

JF - GigaByte

ER -

Genome assembly of the milky mangrove Excoecaria agallocha

Abstract

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