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A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome
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Metadata
Document Title
A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome
Author
Pootakham W, Sonthirod C, Naktang C, Kongkachana W, U-thoomporn S, Phetchawang P, Maknual C, Jiumjamrassil D, Pravinvongvuthi T, Tangphatsornruang S
Name from Authors Collection
Scopus Author ID
57201312649
Scopus Author ID
57199231749
Scopus Author ID
56030033100
Affiliations
National Science & Technology Development Agency - Thailand
Type
Article
Source Title
G3-GENES GENOMES GENETICS
ISSN
2160-1836
Year
2022
Volume
12
Issue
10
Open Access
gold, Green Published
Publisher
OXFORD UNIV PRESS INC
DOI
10.1093/g3journal/jkac025
Format
Abstract
Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves' unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.
Keyword
10x Genomics | Ceriops zippeliana | Chromosome-scale genome assembly | Mangrove | RagTag
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
Rights
Authors
Publication Source
WOS