Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza

Shearman, Jeremy R.; Naktang, Chaiwat; Sontirod, Chutima; Kongkachana, Wasitthee; U‐thoomporn, Sonicha; Jomchai, Nukoon; Maknual, Chatree; Yamprasai, Suchart; Promchoo, Waratthaya; Ruang-areerate, Panthita; Pootakham, Wirulda; Tangphatsornruang, Sithichoke

doi:10.1016/j.ygeno.2022.110382

Cited by 5 publications

(2 citation statements)

References 35 publications

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“…ex Griff.] (Pootakham et al., 2022b) , B. cylindrica (Shearman et al, 2022) (https://www.nstda.or.th/noc/research-development/80-about-us/102-our-genome-assemblies.html, B. gymnorhiza (Yamanaka et al., 2009), upriver orange mangrove [ Bruguiera sexangula (Lour.) Poir.]…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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Mangrove ecosystems are unique, highly diverse, provide benefits to humans, and aid in coastal protection. The Indian mangrove, or spurred mangrove, [Ceriops tagal (Perr.) C. B. Rob.] is a member of the Rhizophoraceae family and is commonly found along the intertidal zones in tropical regions in Southeast Asia, southern Asia, and Africa. Here, we present the first high‐quality reference genome assembly of the Ceriops species. A preliminary draft assembly, generated from the 10× Genomics linked‐read library, was scaffolded using the proximity ligation chromatin contact mapping technique (Hi‐C) to obtain a chromosome‐scale assembly of 231,919,005 bases with an N50 length of 11,408,429 bases. The benchmarking universal single‐copy orthologs (BUSCO) analysis revealed that C. tagal gene predictions recovered 95.8% of the highly conserved orthologs. Phylogenetic analyses suggested that C. tagal diverged from the last common ancestor of flat‐leaf spurred mangrove [C. decandra (Griff.) Ding Hou] and C. zippeliana Blume ∼10.4 million yr ago (MYA), and the last common ancestor of genera Ceriops, Kandelia, and Rhizophora diverged from that of genus Bruguiera ∼49.4 MYA. In addition, our analysis of the transversion rate at fourfold‐degenerate sites from orthologous gene pairs provided evidence supporting a recent whole‐genome duplication in C. tagal. The STRUCTURE and principal component analyses illustrated that C. tagal individuals investigated in this study were the admixture of two subpopulations, the genetic background of which was influenced primarily by location. The availability of genomic and transcriptomic resources and biodiversity data reported in this work will be useful for future studies that may shed light on adaptive evolutions of mangrove species.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2022

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“…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 ].…”

Section: Introductionmentioning

confidence: 99%

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

Naktang

Khanbo

Yundaeng

et al. 2023

Biology

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Unique and biodiverse, mangrove ecosystems provide humans with benefits and contribute to coastal protection. Rhizophora mucronata, a member of the Rhizophoraceae family, is prevalent in the mangrove forests of Thailand. R. mucronata’s population structure and genetic diversity have received scant attention. Here, we sequenced the entire genome of R. mucronata using 10× Genomics technology and obtained an assembly size of 219 Mb with the N50 length of 542,540 bases. Using 2857 single nucleotide polymorphism (SNP) markers, this study investigated the genetic diversity and population structure of 80 R. mucronata accessions obtained from the mangrove forests in Thailand. The genetic diversity of R. mucronata was moderate (I = 0.573, Ho = 0.619, He = 0.391). Two subpopulations were observed and confirmed from both population structure and principal component analysis (PCA). Analysis of molecular variance (AMOVA) showed that there was more variation within populations than between them. Mean pairwise genetic differentiation (FST = 0.09) showed that there was not much genetic difference between populations. Intriguingly, the predominant clustering pattern in the R. mucronata population did not correspond to the Gulf of Thailand and the Andaman Sea, which are separated by the Malay Peninsula. Several factors could have influenced the R. mucronata genetic pattern, such as hybridization and anthropogenic factors. This research will provide important information for the future conservation and management of R. mucronata in Thailand.

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OMICS strategies: Revealing the enigma of salinity tolerance in mangroves

Henna Parveen,

Muhammed,

Sneha

et al. 2024

Crop Design

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Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza

Cited by 5 publications

References 35 publications

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

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

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

OMICS strategies: Revealing the enigma of salinity tolerance in mangroves

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