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The complete mitochondrial genome sequence of Aquilaria sinensis.

ABSTRACT: Aquilaria sinensis, endemic to China, is an economically important evergreen tree species and a source of agarwood. Due to the high market demand for agarwood, this species is heavily overexploited in the wild and is now listed as an endangered species. Although its nuclear and chloroplast genomes have been previously reported, little is known about its mitochondrial genome. Using the paired-end short reads generated by the Illumina sequencing platform, we assembled and herein report the mitochondrial genome of A. sinensis for future phylogenetic, evolutionary, and preservative studies. The length of the A. sinensis mitochondrial genome was found to be 341,829 bp and the GC content was 45.01%. A total of 32 protein-coding genes, 19 tRNA genes, and three rRNA genes were annotated. The phylogenetic tree indicated that A. sinensis is most closely genetically related to Vigna radiata.

SUBMITTER: Wang ZF

PROVIDER: S-EPMC7889115 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Aquilaria sinensis (Lour.) Gilg is an important medicinal woody plant producing agarwood, which is widely used in traditional Chinese medicine. High-throughput sequencing of chloroplast (cp) genomes enhanced the understanding about evolutionary relationships within plant families. In this study, we determined the complete cp genome sequences for A. sinensis. The size of the A. sinensis cp genome was 159,565 bp. This genome included a large single-copy region of 87,482 bp, a small single-copy region of 19,857 bp, and a pair of inverted repeats (IRa and IRb) of 26,113 bp each. The GC content of the genome was 37.11%. The A. sinensis cp genome encoded 113 functional genes, including 82 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. A total of 45 polymorphic simple-sequence repeat loci and 60 pairs of large repeats were identified. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited high A/T content. Moreover, 33 pairs of large repeat sequences were located in the protein-coding genes, whereas 27 pairs were located in the intergenic regions. Aquilaria sinensis cp genome bias ended with A/T on the basis of codon usage. The distribution of codon usage in A. sinensis cp genome was most similar to that in the Gonystylus bancanus cp genome. Comparative results of 82 protein-coding genes from 29 species of cp genomes demonstrated that A. sinensis was a sister species to G. bancanus within the Malvales order. Aquilaria sinensis cp genome presented the highest sequence similarity of >90% with the G. bancanus cp genome by using CGView Comparison Tool. This finding strongly supports the placement of A. sinensis as a sister to G. bancanus within the Malvales order. The complete A. sinensis cp genome information will be highly beneficial for further studies on this traditional medicinal plant. Moreover, the results will enhance our understanding about the evolution of cp genomes of the Malvales order, particularly with regard to the role of A. sinensis in plant systematics and evolution.

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The complete mitochondrial genome sequence of Aquilaria sinensis.

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