Abstract
The entire chloroplast genome of Aquilaria sinensis (Lour.) Gilg was identified as a circular molecule of 174,885 bp length with a typical tetrad structure, including a pair of inverted repeats (42,103 bp each), a large single copy (87,331 bp) and a small single copy (3,348 bp) regions. The A. sinensis cp genome encoded 8 rRNAs, 39 tRNAs, and 90 proteins. A phylogenetic tree was reconstructed using the 43 protein-coding genes of eight Thymelaeaceae. Two other Malvales, Abelmoschus esculentus and Durio zibethinus, were selected as the outgroup. Our phylogenetic analysis suggests that the five examined species of Aquilaria appeared a monophyletic group with robust support.
Keywords: Aquilaria sinensis, Thymelaeaceae, agarwood, chloroplast genome, conservation
Main text
Aquilaria sinensis (Lour.) Gilg belongs to the order Malvales, family Thymelaeaceae. The species has been heavily exploited for its fragrant resin-filled heartwood known as agarwood, which has resulted in declines of at least 30% in the past 10 years. It is assumed that the population was either stable or declining prior to the last 10 years, leading to at least a 30% decline over the last three generations of this species (Harvey-Brown 2018). IUCN (International Union for Conservation of Nature and Natural Resources) therefore assessed this species as vulnerable. Genome resource banking of Aquilaria species would provide useful information for conservation actions such as to establish species in harvest and trade management. Hence, we complete an entire chloroplast (cp) genome sequence of A. sinensis to enrich the genomic resource for further conservation and evolution researches.
The fresh leaves were collected from a ca. 30-year-old A. sinensis tree growing in a private botanical garden in Chia-Yi, Taiwan. The voucher specimens (HAST#142367) were deposited in the Herbarium of Academia Sinica, Taipei, Taiwan. Genomic DNA was extracted from fresh leaves by using a CTAB-based protocol (Stewart and Via 1993). A paired-end library was constructed and then sequenced using the Illumina HiSeq 4000 sequencer (Illumina, San Diego, CA). The 49.36 million clean paired-end reads were assembled and analyzed through the use of CLC Genomics Workbench 12.0 (www.qiagenbioinformatics.com/), Bowtie2 (Langmead and Salzberg 2012), and SAMtools 1.9 (Li et al. 2009). The entire cp genome of A. sinensis has been annotated by DOGMA (Wyman et al. 2004), tRNAscan-SE 1.21 (Schattner et al. 2005) and BLAST searches (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The cp genome sequence of A. sinensis was submitted to DDBJ with the accession number of LC491571.
The complete cp genome of A. sinensis has a circular structure with 174,852 bp in length that is similar to those of Aquilaria yunnanensis (174,885 bp; NCBI accession number: NC_036940), Aquilaria crassna (174,830 bp; NCBI accession number: MK779998), and Aquilaria malaccensis (174,832 bp; NCBI accession number: MH286934). The A. sinensis cp genome contained two inverted repeat regions of 42,103 bp each, separated by a large single-copy region of 87,331 bp and a small single-copy region of 3,348 bp. The contents of A, T, C, and G in the A. sinensis cp genome were found to be 31.5, 36.7, 18.7, and 18.0%, respectively. The A. sinensis cp genome encoded 8 rRNAs, 39 tRNAs, and 90 proteins. Of those genes, rps8 and rps19 were proposed to have a putative start codon, GTG.
The DNA sequences of 43 common protein-coding genes from eight Thymelaeaceae were concatenated for phylogenetic analysis. Two other Malvales, Abelmoschus esculentus and Durio zibethinus, were selected as the outgroup. The best-fit, GTR + G + I, nucleotide substitution model was employed in plant cp genome phylogenetic reconstruction. A maximum-likelihood tree was reconstructed using MEGA7 program (Kumar et al. 2016) with 1000 bootstrap replicates. The five examined species of Aquilaria appeared a monophyletic group with robust support (Figure 1). Our study would provide useful genomic resource for further studies in A. sinensis conservation and evolution.
Figure 1.
The cp genome phylogenetics of Thymelaeaceae. A maximum-likelihood tree inferred from analysis of a data set containing 43 concatenated protein-coding genes in 10 plastomic taxa by use of the GTR + I + G model. Numbers at each node indicate bootstrap support. GenBank accession numbers of the species used in this phylogenetic tree are enclosed in brackets.
Acknowledgements
We thank Mr. Wen-Zhang Shen’s botanical garden for providing plant materials. We are grateful to the Academia Sinica Computing Center for computing resource. We are also immensely grateful to Dr. Yu-Ming Ju for his comments.
Disclosure statement
No potential conflict of interest was reported by the authors.
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