Chromosomal-level genome assembly and single-nucleotide polymorphism sites of black-faced spoonbill Platalea minor

Author:

,Hui Jerome H. L.1ORCID,Chan Ting Fung2ORCID,Chan Leo Lai3ORCID,Cheung Siu Gin4ORCID,Cheang Chi Chiu56ORCID,Fang James Kar-Hei7ORCID,Gaitan-Espitia Juan Diego8ORCID,Lau Stanley Chun Kwan9ORCID,Sung Yik Hei1011ORCID,Wong Chris Kong Chu12ORCID,Yip Kevin Yuk-Lap1314ORCID,Wei Yingying15ORCID,So Wai Lok1ORCID,Nong Wenyan1ORCID,Law Sean Tsz Sum1ORCID,Crow Paul16,Leong Aiko16,Rose-Jeffreys Liz16,Yip Ho Yin1ORCID

Affiliation:

1. Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Hong Kong SAR, China

2. 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. 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, CA, La Jolla, USA

15. Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China

16. Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong SAR, China

Abstract

Platalea minor, or black-faced spoonbill (Threskiornithidae), is a wading bird confined to coastal areas in East Asia. Due to habitat destruction, it was classified as globally endangered by the International Union for Conservation of Nature. However, the lack of genomic resources for this species hinders the understanding of its biology and diversity, and the development of conservation measures. Here, we report the first chromosomal-level genome assembly of P. minor using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (1.24 Gb) contains 95.33% of the sequences anchored to 31 pseudomolecules. The genome assembly has high sequence continuity with scaffold length N50 = 53 Mb. We predicted 18,780 protein-coding genes and measured high BUSCO score completeness (97.3%). Finally, we revealed 6,155,417 bi-allelic single nucleotide polymorphisms, accounting for ∼5% of the genome. This resource offers new opportunities for studying the black-faced spoonbill and developing conservation measures for this species.

Funder

Hong Kong Research Grant Council Collaborative Research Fund

CUHK Strategic Seed Funding for Collaborative Research Scheme

CUHK Group Research Scheme

Publisher

GigaScience Press

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