A chromosome-scale reference genome assembly of yellow mangrove (Bruguiera parviflora) reveals a whole genome duplication event associated with the Rhizophoraceae lineage.

Mangrove forest ecosystems support a diverse flora and fauna of marine and terrestrial species and have important direct and indirect economic, ecological and social values to mankind. Yellow mangrove (Bruguiera parviflora) belongs to the Rhizophoraceae family and is widely distributed in the intertidal zones along sheltered coastal areas in tropical latitudes. Here, we present a high-quality, chromosome-level assembly of the B. parviflora genome. We employed the 10x Genomics linked-read technology to obtain a preliminary assembly, which was subsequently scaffolded using the long-range chromatin contact mapping technique (HiC) to obtain a final assembly containing 213,026,782 bases in 10,045 scaffolds with an N50 length of 10,906,948 bases. Our gene prediction recovered 96.5% of the highly conserved orthologues in the Embryophyta lineage based on the Benchmarking Universal Single-Copy Orthologues (BUSCO) analysis. We analysed the transversion rate at fourfold-degenerate sites from orthologous gene pairs and discovered evidence supporting a recent whole-genome duplication event in B. parviflora and other Rhizophoreae members. Comparative studies based on single-copy orthologous genes indicated that B. parviflora and Bruguiera gymnorrhiza diverged approximately 24.1 million years ago. The population structure analysis revealed that 63 B. parviflora accessions from different geographical regions in Thailand were an admixture of two subpopulations. The examination of alternative splicing events in B. parviflora showed that the most prevalent splicing mechanism was intron retention. This high-quality genome assembly together with the genetic diversity information obtained from the germplasm provide useful genomic resources for future studies on comparative phylogenetics and evolution of adaptive traits in mangrove species.

Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships.

Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.