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De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome
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Document Title
De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome
Author
Pootakham W, Naktang C, Sonthirod C, Kongkachana W, Yoocha T, Jomchai N, Maknual C, Chumriang P, Pravinvongvuthi T, Tangphatsornruang S
Name from Authors Collection
Scopus Author ID
57201312649
Scopus Author ID
56030033100
Scopus Author ID
36059124300
Affiliations
National Science & Technology Development Agency - Thailand
Type
Article
Source Title
GENOME BIOLOGY AND EVOLUTION
ISSN
1759-6653
Year
2022
Volume
14
Open Access
gold, Green Published
Publisher
OXFORD UNIV PRESS
DOI
10.1093/gbe/evac025
Format
Abstract
Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10x Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bases. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves' physiological and morphological adaptations to the intertidal zones.
Keyword
10x | Bruguiera sexangula | genome assembly | Genomics | Mangrove
Industrial Classification
Knowledge Taxonomy Level 1
Knowledge Taxonomy Level 2
Knowledge Taxonomy Level 3
Funding Sponsor
National Science and Technology Development Agency (NSTDA), Thailand [P-19-52261]
License
CC BY-NC
Rights
Authors
Publication Source
WOS