Abstract
The complete mitochondrial genome of mangrove plant Bruguiera sexangula was analyzed in this paper, which is the first for the genus within the family Rhizophoraceae. The mitogenome sequence is 303,026 bp in length containing 3 ribosomal RNA genes, 20 transfer RNA genes, and 37 protein-coding genes. Genes ccmFc, rps3, and cox2 contain one intron each, genes nad1 and nad5 contain two introns each, gene nad4 contains three introns and gene nad2 and nad7 contain four introns each. Gene nad1, nad2, and nad5 are trans-splicing genes. Phylogenetic analysis using the maximum-likelihood method positioned B. sexangula closely with Citrus sinensis.
Bruguiera sexangula belonging to Rhizophoraceae species has a wide distribution from India, Malay, Sri Lanka, Thailand, and Vietnam to South China (Wang and Wang Citation2006). Bruguiera sexangula is usually found in upstream reaches of river-dominated estuaries in high rainfall areas (Tomlinson Citation2016). Bruguiera sexangula is distinguished from other Bruguiera by: large solitary-flowered inflorescence with petals having a spine slightly shorter than the paired lobes and blunt petal lobes with a single minute or absent bristles, and relatively short hypocotyls (Duck Citation2006). Mitochondrial genome-based phylogenetic analysis would improve our understanding of the evolutionary relationship of this plant under tidal habitat. In this study, we sequenced and analyzed the complete mitochondrial DNA sequence of B. sexangula. This is the first complete mitogenome within the family Rhizophoraceae or even in Malpighiales.
Fresh leaves were collected from three individual of B. sexangula in Dongzhai Harbor Mangrove Natural Garden, Hainan Island (N19°51′∼20°01′, E110°32′∼110°37′), China. The total genomic DNA was extracted from ten mixed fresh leaves of B. sexangula by using the modified CTAB method (Doyle Citation1987) in the laboratory of Hainan Normal University. Further, the specimen was also stored in the herbarium of Hainan Normal University (No. Sp20190701-005). Genome sequencing was performed on an Illumina Hiseq X Ten platform with paired-end reads of 150 bp. In total, 54.3 Gb short sequence data with Q20 was 95.83% was obtained. The remaining high-quality reads were used to assemble the mitogenome by NOVOPlasty (Dierckxsens et al. Citation2017), where Arabidopsis thaliana (GenBank accession NC_037304.1) used as the seed sequence. The gene annotation in the mitogenome was doing with SPAdes v.3.9.0 (Bankevich et al. Citation2012) and some genes were annotated manually. The accession number in Genbank is MT130510. Six mitogenome sequences were aligned including B. sexangula, Oryza sativa was used as the out-group species. Phylogenetic analysis using the maximum likelihood algorithm was conducted with Mega X (Kumar et al. Citation2018).
The mitogenome of B. sexangula is 303,026 bp in length with GC content of 44.27%, which contains three ribosomal RNA genes (rrn5, rrn18, and rrn26), 20 transfer RNA genes, and 37 protein-coding genes. Among those genes, ccmFc, rps3, and cox2 contain one intron, gene nad1 and nad5 contain two introns, gene nad4 contains three introns and gene nad2 and nad7 contain four introns. Gene nad1, nad2, and nad5 are trans-splicing genes. Phylogenetic analysis with the other five plant mitogenomes showed that B. sexangula is closest to Citrus sinensis (). The useful genomic resources for the characterization of the genetic diversity of B. sexangula by the mitogenome will help for the study of the evolution mechanism.
Figure 1. Maximum-likelihood tree based on the sequences of seven complete mitogenomes. Numbers in the nodes were bootstrap values from 1000 replicates. Scale in substitutions per site.
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No potential conflict of interest was reported by the author(s).
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References
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