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

Abstract

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.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

“…Ceriops and Avicennia have a convergent evolution and are the most dominant species in the middle and seaward zones of mangrove forests, respectively [1, 3,24]. The three Ceriops chloroplast genomes (164.4-166.7 kb) were slightly different, consistent with published chloroplast genomes of mangrove species (middle zone) in Rhizophoraceae such as C. tagal, Kandelia obovata, Rhizophora species, and Bruguiera species (160.3-164.6 kb) [40][41][42][65][66][67]. In contrast, the smaller chloroplast genome of A. lanata was 148.2 kb, which is similar to the previously reported chloroplast genome of Avicennia marina (147.9-152.3 kb) [39,68].…”

“…Diverse chloroplast genome sequences have been used to study the evolution of mangrove species and to identify different mangrove species [39][40][41][42]. In the current study, we reported the chloroplast genomes of four mangrove species, including three Ceriops species (C. decandra, C. zippeliana, and C. tagal) and Avicennia lanata.…”

“…Nevertheless, gene gain and loss have been found among the four mangrove species. The infA gene (translation initiation factor 1) was found in A. lanata but not in the Ceriops species and other mangrove species in Rhizophoraceae [40][41][42]. The loss of the infA gene from the chloroplast to the nucleus occurred independently in multiple angiosperm lineages, especially in Rosids [73,74].…”

“…Chloroplast genomes are highly conserved because of uni-parent inheritance or maternal inheritance [38]. The sizes of chloroplast genomes in mangrove species are around 145-168 kb [39][40][41][42]. Chloroplast genomes in mangrove species usually contain four regions, including one large single-copy region (LSC), two inverted repeats (IRA and IRB), and one single small-copy region (SSC) [39][40][41][42].…”

“…The sizes of chloroplast genomes in mangrove species are around 145-168 kb [39][40][41][42]. Chloroplast genomes in mangrove species usually contain four regions, including one large single-copy region (LSC), two inverted repeats (IRA and IRB), and one single small-copy region (SSC) [39][40][41][42]. To date, several chloroplast genomes have been reported because of the development of DNA sequencing technology and bioinformatics methods [43][44][45].…”