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

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 bp. 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 (GO) 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.

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

“…The slight difference in the genome size estimated by DNA flow cytometry (236 Mb) and the assembly size likely reflected the unassembled repetitive portions of the genome. The number of predicted gene models in C. tagal genome (23,658) was lower than the figure reported for R. apiculata (26,640) (Xu et al., 2017), higher than the number reported for K. obovata (19,138) (Hu et al., 2020), and similar to that reported in B. parviflora (22,421) (Pootakham et al., 2022). In terms of GO assignment, 85.8 and 83.3% of C. tagal and B. parviflora protein‐coding sequences were associated with GO terms, while lower proportions of K. obovata (78.8%) and R. apiculata (60%) protein‐coding genes were assigned GO terms.…”

“…Genomic DNA was isolated using the CTAB method previously described in Pootakham et al. (2022a). The amount and integrity of the DNA samples were checked using the Qubit fluorometer (ThermoFisher Scientific).…”

“…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 (Pootakham et al., 2022a), C. decandra (unpublished data, 2022) (https://www.ncbi.nlm.nih.gov/assembly/GCA_020615895.1/), C. zippeliana (Pootakham et al., 2022c), K. obovata (Hu et al., 2020), and R. apiculata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).…”

“…We also collected leaf samples from 66 accessions distributed in mangrove forests across multiple provinces in Thailand: Chachoengsao (CCO), Chantaburi (CTI), Chumphon (CMP), Pattani (PTN), Petchaburi (PBI), Phangnga (PNA), Phuket (PKT), Prachuap Khiri Khan (PKN), Ranong (RNG), Satun (STN), Surat Thani (SNI), and Trat (TRT) (Supplemental Figure S1, Supplemental Table S1). Genomic DNA was isolated using the CTAB method previously described in Pootakham et al (2022a). The amount and integrity of the DNA samples were checked using the Qubit fluorometer (ThermoFisher Scientific).…”

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 ].…”