A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome

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 (GO) terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) 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.

Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species

“…Poir.] (Pootakham et al., 2022a), C. decandra (unpublished data, 2022) (https://www.ncbi.nlm.nih.gov/assembly/GCA_020615895.1/), C. zippeliana (Pootakham et al., 2022c), K. obovata (Hu et al., 2020), and R. apiculata (Xu et al., 2017)}, five dicots [ Arabidopsis , melon ( Cucumis melo L.), cucumber ( Cucumis sativus L.), castor ( Ricinus communis L.), and P. trichocarpa ]; and one monocot (rice). A phylogenetic tree was constructed based on protein sequences from single‐copy orthologous groups using the RAxML‐NG program v1.0.2 (Stamatakis, 2006).…”

Assessment of the Genetic Diversity and Population Structure of Rhizophora mucronata along Coastal Areas in Thailand

“…Over the past decade, the advances in sequencing technologies have provided genomic information to study population genetics in mangroves. A number of reference genomes of species in the family Rhizophoraceae have been reported [ 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Various molecular markers have been utilized to assess the genetic diversity of mangrove species, including amplification fragment length polymorphism (AFLP) [ 30 ], simple sequence repeats (SSR) [ 31 , 32 ] and randomly amplified polymorphic DNA (RADP) [ 33 ].…”

De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome

“…In an attempt to understand the molecular basis of mangroves’ physiological adaptations in order to better conserve and restore mangrove ecosystems, multiple mangrove genomes have been sequenced including Rhizophora apiculata ( Xu et al 2017 ), Kandelia obovata ( Hu et al 2020 ), Bruguiera parviflora ( Pootakham, Sonthirod, Naktang, Kongkachana, Sangsrakru, et al 2022 ) and Ceriops zippeliana ( Pootakham, Sonthirod, Naktang, Kongkachana, U-Thoomporn, et al 2022 ) from the Rhizophoraceae family, Avicenna marina ( Friis et al 2021 ) from the Acanthaceae family, and Aegiceras corniculatum ( Feng et al 2021 ) from the Primulaceae family. Transcriptomic resources from various mangrove species have also been reported in the past few years ( Yamanaka et al 2009 ; Yang Y, Yang S, Li, Deng, et al 2015 , Yang Y, Yang S, Li J, Li X, et al 2015 ; Krishnamurthy et al 2017 ; Xu et al 2017 ).…”