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

Abstract

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.

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

“…Most of the retrotransposons were classified as long terminal repeats (39.76 Mb), which could further be categorized into Copia -like (15.60 Mb) and Gypsy -like (19.07 Mb) elements ( supplementary table 4, Supplementary Material online). The percentage of the B. sexangula assembly containing repetitive elements (38.2%) was higher than that observed in the K. obovata (24%) ( Hu et al 2020 ), B. parviflora (26%) ( Pootakham, Sonthirod, Naktang, Kongkachana, Sangsrakru, et al 2022 ) and R. apiculata (29%) ( Xu et al 2017 ) genomes but comparable to the figure reported for the Populus trichocarpa genome (40%) ( Zhou and Xu 2009 ).…”

“…The preliminary assembly generated from the linked-read data was 263,981,354 bases with an N50 contig length of 1,414,200 bases ( table 1 ). This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related mangrove species, B. parviflora ( Pootakham, Sonthirod, Naktang, Kongkachana, Sangsrakru, et al 2022 ), as a reference. The final assembly contained 260,518,658 bases in 20,644 scaffolds with an N50 length of 11,020,310 bases ( fig.…”

“…Linked-read data were assembled using the Supernova assembler v2.1.1 using the default settings ( https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/running ; last accessed: February 14, 2022 ; 10× Genomics, Pleasanton, USA). The preliminary assembly was further scaffolded with RagTag v1.1.0 ( https://github.com/malonge/RagTag ; last accessed: February 14, 2022) ( Alonge et al 2019 ) using the B. parviflora genome assembly ( Pootakham, Sonthirod, Naktang, Kongkachana, Sangsrakru, et al 2022 ), as a reference.…”

“…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 ).…”

“…In this work, we employed the 10× Genomics linked-read technology ( Paajanen et al 2019 ) to obtain a draft assembly of the B. sexangula genome. We subsequently utilized RagTag software to scaffold this preliminary assembly using a chromosome-level genome assembly of a closely related mangrove species, B. parviflora ( Pootakham, Sonthirod, Naktang, Kongkachana, Sangsrakru, et al 2022 ), as a reference. We also obtained transcript data (RNA-seq) to assist with coding gene prediction and annotation.…”