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

PeerJ

article

Panthita Ruang-areerate¹  Wasitthee Kongkachana¹  Chaiwat Naktang¹  Chutima Sonthirod¹  Nattapol Narong¹  Nukoon Jomchai¹  Pasin Maprasop²  Chatree Maknual²  Nawin Phormsin²  Jeremy R. Shearman¹  Wirulda Pootakham¹  Sithichoke Tangphatsornruang¹ 

[1]National Omics Center, National Science and Technology Development Agency

[2]Department of Marine and Coastal Resources

关键词: Bruguiera;    Mangrove;    Chloroplast genome;    Rhizophoraceae;    Comparative analysis;    Phylogenetic relationships;   

DOI  :  10.7717/peerj.12268

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY