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

2024/07/18 by Jerome H. L. Hui, Ting‐Fung Chan, Leo Lai Chan +16 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Identification and Quantification in Food

paper · pdf · doi:10.46471/gigabyte.130

openalex publication_date 2024/07/18 · openalex created_date 2024/07/19 · openalex updated_date 2026/08/01

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.

Citations

• Synteny and Collinearity in Plant Genomes
• A framework for variation discovery and genotyping using next-generation DNA sequencing data
• Identifying and removing haplotypic duplication in primary genome assemblies
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• YaHS: yet another Hi-C scaffolding tool
• Chromosome-level genome of the wood stork (Mycteria americana) provides insight into avian chromosome evolution
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Discussions

• New paper from the Hong Kong Biodiversity Genomics Consortium presenting the genome of an iconic, endangered, East Asian bird species. Chromosomal-level genome assembly and single-nucleotide polymorp [bsky, 0 points, 0 comments]