Genome assembly of the milky mangrove Excoecaria agallocha

Hong Kong Biodiversity Genomics Consortium; 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

doi:10.46471/gigabyte.119

Genome assembly of the milky mangrove Excoecaria agallocha

Hong Kong Biodiversity Genomics Consortium
, 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

Science Unit

Research output: Journal Publications › Journal Article (refereed) › 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
Journal	GigaByte
Volume	2024
DOIs	https://doi.org/10.46471/gigabyte.119
Publication status	Published - 2024

Bibliographical note

Publisher Copyright:
© 2024 GigaScience Press. All rights reserved.

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).

UN SDGs

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

SDG 11 Sustainable Cities and Communities
SDG 15 Life on Land

Keywords

Botany
Genetics and Genomics
Plant Genetics

Access to Document

10.46471/gigabyte.119

Cite this

Hong Kong Biodiversity Genomics Consortium, 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. (2024). Genome assembly of the milky mangrove Excoecaria agallocha. GigaByte, 2024. https://doi.org/10.46471/gigabyte.119

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title = "Genome assembly of the milky mangrove Excoecaria agallocha",

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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author = "\{Hong Kong Biodiversity Genomics Consortium\} and HUI, \{Jerome H.L.\} and CHAN, \{Ting Fung\} and CHAN, \{Leo Lai\} and CHEUNG, \{Siu Gin\} and CHEANG, \{Chi Chiu\} and FANG, \{James Kar Hei\} and GAITAN-ESPITIA, \{Juan Diego\} and LAU, \{Stanley Chun Kwan\} and SUNG, \{Yik Hei\} and WONG, \{Chris Kong Chu\} and YIP, \{Kevin Yuk Lap\} and Yingying WEI and LAW, \{Sean Tsz Sum\} and SO, \{Wai Lok\} and Wenyan NONG and LAU, \{David Tai Wai\} and LEE, \{Shing Yip\} and YIP, \{Ho Yin\}",

year = "2024",

doi = "10.46471/gigabyte.119",

language = "English",

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T1 - Genome assembly of the milky mangrove Excoecaria agallocha

AU - Hong Kong Biodiversity Genomics Consortium

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

PY - 2024

Y1 - 2024

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

UR - https://www.scopus.com/pages/publications/85193687412

U2 - 10.46471/gigabyte.119

DO - 10.46471/gigabyte.119

M3 - Journal Article (refereed)

C2 - 38707633

AN - SCOPUS:85193687412

SN - 2709-4715

VL - 2024

JO - GigaByte

JF - GigaByte

ER -

Genome assembly of the milky mangrove Excoecaria agallocha

Abstract

Bibliographical note

Funding

UN SDGs

Keywords

Access to Document

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